Hello, pardon me for having so many questions but I am new to gromacs, especially to martini forcefield operations.
**My main concern in all of this is when do I know which .mdp file to use in the tutorial for energy minimization. 2) what is wrong with the problem that my molecule numbers aren't matching when running energy minimization after I have solvated the system? ******

But as I was following the protein in water tutorial md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water
in STEP 4 to 5.

It says that do a (+/-10) step of energy minimization in vacuum, I did the following:

editconf -f cg_1UBQ.pdb -o cg_1UBQ_box.pdb -c -d 1.0 -bt cubic

grompp -f md.mdp -c cg_1UBQ_box.pdb -p system.top -o em.tpr

*I get the following error from using md.mdp supplied by the tutorial zip
[Replacing old mdp entry 'unconstrained_start' by 'continuation'

NOTE 1 : nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' Analysing residue names: There are: 76 Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group System is 456.00 This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning] ***(I then re-did the grompp using a different energy minim.mdp file from another source which excludes martini parameters I'm assuming, and it ran and produced the 3 files of em.trr, em.edr em.log em.gro. Someone please correct me and tell me that I shouldn't have used a third party source minim.mdp file instead of the martini defined md.mdp since i'm working with a coarse grained structure here, if so what should I do? is there something wrong with the md.mdp supplied?) The minim.mdp i used contained the following: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) *This is the output of MDRUN Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= 3.87916e+02 Fmax= 3.76519e+04, atom= 131 Step= 1, Dmax= 1.0e-02 nm, Epot= -6.03755e+02 Fmax= 1.76086e+04, atom= 131 Step= 2, Dmax= 1.2e-02 nm, Epot= -1.60632e+03 Fmax= 7.53910e+03, atom= 131 Step= 3, Dmax= 1.4e-02 nm, Epot= -2.63159e+03 Fmax= 3.14060e+03, atom= 122 Step= 4, Dmax= 1.7e-02 nm, Epot= -3.55170e+03 Fmax= 1.65191e+03, atom= 41 Step= 5, Dmax= 2.1e-02 nm, Epot= -4.20992e+03 Fmax= 8.59476e+02, atom= 41 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 6 steps Potential Energy = -4.2099199e+03 Maximum force = 8.5947614e+02 on atom 41 Norm of force = 3.9169992e+02 ------------------------------------------------------------------------------------------ But the more interesting part is when I try to do step 5 which says solvate the system using the pre-equiliberated water-1bar-303K.gro I did the following: genbox -cp em.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro -p system.top *My output says the following: Output configuration contains 1800 atoms in 1713 residues Volume : 241.165 (nm^3) Density : 2104.75 (g/l) Number of SOL molecules: 0 then I run energy minimization on the solvated.gro grompp -f md.mdp -c solvated.gro -p system.top -o em2.tpr I get the following with mismatch: ------------------------------- NOTE 1 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (solvated.gro, 1800) does not match topology (system.top, 163) (AGAIN, here, should I not be using md.mdp or something? i don't know what I am doing wrong. I am trying to follow the tutorial, but I'm hitting a snag everywhere, let me know if you can point me in the right direction. Thanks)[file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy


NOTE 2 : The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' Analysing residue names: There are: 76 Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group System is 456.00 This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning] ***(I then re-did the grompp using a different energy minim.mdp file from another source which excludes martini parameters I'm assuming, and it ran and produced the 3 files of em.trr, em.edr em.log em.gro. Someone please correct me and tell me that I shouldn't have used a third party source minim.mdp file instead of the martini defined md.mdp since i'm working with a coarse grained structure here, if so what should I do? is there something wrong with the md.mdp supplied?) The minim.mdp i used contained the following: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) *This is the output of MDRUN Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= 3.87916e+02 Fmax= 3.76519e+04, atom= 131 Step= 1, Dmax= 1.0e-02 nm, Epot= -6.03755e+02 Fmax= 1.76086e+04, atom= 131 Step= 2, Dmax= 1.2e-02 nm, Epot= -1.60632e+03 Fmax= 7.53910e+03, atom= 131 Step= 3, Dmax= 1.4e-02 nm, Epot= -2.63159e+03 Fmax= 3.14060e+03, atom= 122 Step= 4, Dmax= 1.7e-02 nm, Epot= -3.55170e+03 Fmax= 1.65191e+03, atom= 41 Step= 5, Dmax= 2.1e-02 nm, Epot= -4.20992e+03 Fmax= 8.59476e+02, atom= 41 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 6 steps Potential Energy = -4.2099199e+03 Maximum force = 8.5947614e+02 on atom 41 Norm of force = 3.9169992e+02 ------------------------------------------------------------------------------------------ But the more interesting part is when I try to do step 5 which says solvate the system using the pre-equiliberated water-1bar-303K.gro I did the following: genbox -cp em.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro -p system.top *My output says the following: Output configuration contains 1800 atoms in 1713 residues Volume : 241.165 (nm^3) Density : 2104.75 (g/l) Number of SOL molecules: 0 then I run energy minimization on the solvated.gro grompp -f md.mdp -c solvated.gro -p system.top -o em2.tpr I get the following with mismatch: ------------------------------- NOTE 1 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (solvated.gro, 1800) does not match topology (system.top, 163) (AGAIN, here, should I not be using md.mdp or something? i don't know what I am doing wrong. I am trying to follow the tutorial, but I'm hitting a snag everywhere, let me know if you can point me in the right direction. Thanks)[file md.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.


WARNING 1 : For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' Analysing residue names: There are: 76 Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group System is 456.00 This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning] ***(I then re-did the grompp using a different energy minim.mdp file from another source which excludes martini parameters I'm assuming, and it ran and produced the 3 files of em.trr, em.edr em.log em.gro. Someone please correct me and tell me that I shouldn't have used a third party source minim.mdp file instead of the martini defined md.mdp since i'm working with a coarse grained structure here, if so what should I do? is there something wrong with the md.mdp supplied?) The minim.mdp i used contained the following: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) *This is the output of MDRUN Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= 3.87916e+02 Fmax= 3.76519e+04, atom= 131 Step= 1, Dmax= 1.0e-02 nm, Epot= -6.03755e+02 Fmax= 1.76086e+04, atom= 131 Step= 2, Dmax= 1.2e-02 nm, Epot= -1.60632e+03 Fmax= 7.53910e+03, atom= 131 Step= 3, Dmax= 1.4e-02 nm, Epot= -2.63159e+03 Fmax= 3.14060e+03, atom= 122 Step= 4, Dmax= 1.7e-02 nm, Epot= -3.55170e+03 Fmax= 1.65191e+03, atom= 41 Step= 5, Dmax= 2.1e-02 nm, Epot= -4.20992e+03 Fmax= 8.59476e+02, atom= 41 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 6 steps Potential Energy = -4.2099199e+03 Maximum force = 8.5947614e+02 on atom 41 Norm of force = 3.9169992e+02 ------------------------------------------------------------------------------------------ But the more interesting part is when I try to do step 5 which says solvate the system using the pre-equiliberated water-1bar-303K.gro I did the following: genbox -cp em.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro -p system.top *My output says the following: Output configuration contains 1800 atoms in 1713 residues Volume : 241.165 (nm^3) Density : 2104.75 (g/l) Number of SOL molecules: 0 then I run energy minimization on the solvated.gro grompp -f md.mdp -c solvated.gro -p system.top -o em2.tpr I get the following with mismatch: ------------------------------- NOTE 1 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (solvated.gro, 1800) does not match topology (system.top, 163) (AGAIN, here, should I not be using md.mdp or something? i don't know what I am doing wrong. I am trying to follow the tutorial, but I'm hitting a snag everywhere, let me know if you can point me in the right direction. Thanks)[file md.mdp]:
For proper integration of the Berendsen barostat, tau_p (1) should be at
least 10 times larger than nstpcouple*dt (0.2)

Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein_A'
Analysing residue names:
There are: 76 Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group System is 456.00
This run will generate roughly 0 Mb of data

There were 2 notes

There was 1 warning]

***(I then re-did the grompp using a different energy minim.mdp file from another source which excludes martini parameters I'm assuming, and it ran and produced the 3 files of em.trr, em.edr em.log em.gro. Someone please correct me and tell me that I shouldn't have used a third party source minim.mdp file instead of the martini defined md.mdp since i'm working with a coarse grained structure here, if so what should I do? is there something wrong with the md.mdp supplied?)

The minim.mdp i used contained the following:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)

*This is the output of MDRUN

Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 3.87916e+02 Fmax= 3.76519e+04, atom= 131
Step= 1, Dmax= 1.0e-02 nm, Epot= -6.03755e+02 Fmax= 1.76086e+04, atom= 131
Step= 2, Dmax= 1.2e-02 nm, Epot= -1.60632e+03 Fmax= 7.53910e+03, atom= 131
Step= 3, Dmax= 1.4e-02 nm, Epot= -2.63159e+03 Fmax= 3.14060e+03, atom= 122
Step= 4, Dmax= 1.7e-02 nm, Epot= -3.55170e+03 Fmax= 1.65191e+03, atom= 41
Step= 5, Dmax= 2.1e-02 nm, Epot= -4.20992e+03 Fmax= 8.59476e+02, atom= 41

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 6 steps
Potential Energy = -4.2099199e+03
Maximum force = 8.5947614e+02 on atom 41
Norm of force = 3.9169992e+02

---

But the more interesting part is when I try to do step 5 which says solvate the system using the pre-equiliberated water-1bar-303K.gro

I did the following:

genbox -cp em.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro -p system.top

*My output says the following:

Output configuration contains 1800 atoms in 1713 residues
Volume : 241.165 (nm^3)
Density : 2104.75 (g/l)
Number of SOL molecules: 0

then I run energy minimization on the solvated.gro

grompp -f md.mdp -c solvated.gro -p system.top -o em2.tpr

I get the following with mismatch:

---

NOTE 1 : nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (solvated.gro, 1800) does not match topology (system.top, 163) (AGAIN, here, should I not be using md.mdp or something? i don't know what I am doing wrong. I am trying to follow the tutorial, but I'm hitting a snag everywhere, let me know if you can point me in the right direction. Thanks)[file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy


NOTE 2 : The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. WARNING 1 [file md.mdp]: For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (solvated.gro, 1800) does not match topology (system.top, 163) (AGAIN, here, should I not be using md.mdp or something? i don't know what I am doing wrong. I am trying to follow the tutorial, but I'm hitting a snag everywhere, let me know if you can point me in the right direction. Thanks)[file md.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.


WARNING 1 : For proper integration of the Berendsen barostat, tau_p (1) should be at least 10 times larger than nstpcouple*dt (0.2) Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein_A' ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (solvated.gro, 1800) does not match topology (system.top, 163) (AGAIN, here, should I not be using md.mdp or something? i don't know what I am doing wrong. I am trying to follow the tutorial, but I'm hitting a snag everywhere, let me know if you can point me in the right direction. Thanks)[file md.mdp]:
For proper integration of the Berendsen barostat, tau_p (1) should be at
least 10 times larger than nstpcouple*dt (0.2)

Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein_A'

---

Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (solvated.gro, 1800)
does not match topology (system.top, 163)

(AGAIN, here, should I not be using md.mdp or something? i don't know what I am doing wrong. I am trying to follow the tutorial, but I'm hitting a snag everywhere, let me know if you can point me in the right direction. Thanks)

djurre wrote: Warnings can be ignored using "-maxwarn 1". But in this case it might be better to set tau_p larger (I mostly use 3.0), as the warning tells you. Don't use the other mdp, since it uses many different options (eg PME).

The second problem, an error which you can't ignore, is because you forgot to add the solvent to your system.top file.

@djurre,

I thought i took care of the adding solvent to my system file when I did the following in my command code:

genbox -cp em.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro -p system.top

*the part -p system.top should have updated the fact that water was added? No?

If not, how do I manually add water into my topology file? and how much? (I think I type W and then the number? or SOL and then the number?

@ djurre

I have a new error problem:

What does this mean? I tried running the mdrun -v -deffnm em2 (energy minimization) of the solvated.gro

step 0Segmentation fault: 11

Is it because my defined solvated water box is not big enough for the protein? I viewed it in VMD, the box seems pretty big for the protein, I don't see a size problem. Let me know.

Thanks

xavier wrote: You need to had the water manually in the topology file.

W 1234 ; should do the trick with 1234 being the number of solvent bead added.

The new error you have says your system is exploding. When this happens at the first step of the minimization it most likely is due to bad contact in the starting structure ... be more careful on the way you construct it and the error should disappear ...

xudongh wrote: @ djurre

I have a new error problem:

What does this mean? I tried running the mdrun -v -deffnm em2 (energy minimization) of the solvated.gro

step 0Segmentation fault: 11

Is it because my defined solvated water box is not big enough for the protein? I viewed it in VMD, the box seems pretty big for the protein, I don't see a size problem. Let me know.

Thanks

What do you mean be more careful of the way the structure is created? Do you mean I should allow more steps during the 1st energy minimization run in a vacuum? (Otherwise the structure is obtained directly from running the martini script )

Let me know, thank you :)

Just as a general question.

How do I know that I have successfully produced a working end product following the tutorial on Protein in Water?

Is there something I can compare to that I did things correctly? Perhaps comparing certain energy of minimized systems?