normal Problem in following MARTINI tutorial

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9 years 2 months ago #737 by naba
I am trying to set a coarse-grained MD for the same protein (1UBQ.pdb) therein the MARTINI tutorial ( md.chem.rug.nl/cgmartini/index.php/tutorial ). After the solvation by water-1bar-303K.gro I tried to minimize the system but it gives the following weired results.


grompp gives the following output:

checking input for internal consistency...
processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
Excluding 1 bonded neighbours molecule type 'W'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
There are: 76 Protein residues
There are: 5199 Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Making dummy/rest group for T-Coupling containing 5362 elements
Making dummy/rest group for Acceleration containing 5362 elements
Making dummy/rest group for Freeze containing 5362 elements
Making dummy/rest group for Energy Mon. containing 5362 elements
Making dummy/rest group for VCM containing 5362 elements
Number of degrees of freedom in T-Coupling group rest is 16053.00
Making dummy/rest group for User1 containing 5362 elements
Making dummy/rest group for User2 containing 5362 elements
Making dummy/rest group for XTC containing 5362 elements
Making dummy/rest group for Or. Res. Fit containing 5362 elements
Making dummy/rest group for QMMM containing 5362 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
This run will generate roughly 2 Mb of data
writing run input file...

But mdrun gives the following output:

Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 5000
Step= 14, Dmax= 1.2e-06 nm, Epot= 3.55783e+18 Fmax= inf, atom= 294
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up solvated.gro to ./#solvated.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 3.5578291e+18
Maximum force = inf on atom 294
Norm of force = 1.0627526e+19

Maximum force is equal to infinity and hence I am afraid to proceed further. Then I deleted all files and started from the beginning. I created mdp files for energy minimization, position restraint and MD separately and tried the same but I got the same results again with "segmentation fault". mdrun executed successfully when I used GROMACS in double precision. Position restraint did not run unless I changed dt= 0.030 to 0.004. But I think something is wrong as it is well-known for MARTINI that most simulations are numerically stable with dt=40 fs, some (especially rings) require 20-30 fs. But in this case position restraint gives "segmentation fault" for dt=0.030.

Please help me. I need to set a huge system with coarse grained methods. This is just the tutorial which I am not able to complete it successfully. please help.

Regards,
Naba

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9 years 2 months ago #740 by xavier
Replied by xavier on topic Problem in following MARTINI tutorial
Many things could have gone wrong at this stage.

Where did you get the mdp file? It is likely the source of errors.

XAvier.

naba wrote: I am trying to set a coarse-grained MD for the same protein (1UBQ.pdb) therein the MARTINI tutorial ( md.chem.rug.nl/cgmartini/index.php/tutorial ). After the solvation by water-1bar-303K.gro I tried to minimize the system but it gives the following weired results.


grompp gives the following output:

checking input for internal consistency...
processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
Excluding 1 bonded neighbours molecule type 'W'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
There are: 76 Protein residues
There are: 5199 Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Making dummy/rest group for T-Coupling containing 5362 elements
Making dummy/rest group for Acceleration containing 5362 elements
Making dummy/rest group for Freeze containing 5362 elements
Making dummy/rest group for Energy Mon. containing 5362 elements
Making dummy/rest group for VCM containing 5362 elements
Number of degrees of freedom in T-Coupling group rest is 16053.00
Making dummy/rest group for User1 containing 5362 elements
Making dummy/rest group for User2 containing 5362 elements
Making dummy/rest group for XTC containing 5362 elements
Making dummy/rest group for Or. Res. Fit containing 5362 elements
Making dummy/rest group for QMMM containing 5362 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
This run will generate roughly 2 Mb of data
writing run input file...

But mdrun gives the following output:

Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 5000
Step= 14, Dmax= 1.2e-06 nm, Epot= 3.55783e+18 Fmax= inf, atom= 294
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up solvated.gro to ./#solvated.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 3.5578291e+18
Maximum force = inf on atom 294
Norm of force = 1.0627526e+19

Maximum force is equal to infinity and hence I am afraid to proceed further. Then I deleted all files and started from the beginning. I created mdp files for energy minimization, position restraint and MD separately and tried the same but I got the same results again with "segmentation fault". mdrun executed successfully when I used GROMACS in double precision. Position restraint did not run unless I changed dt= 0.030 to 0.004. But I think something is wrong as it is well-known for MARTINI that most simulations are numerically stable with dt=40 fs, some (especially rings) require 20-30 fs. But in this case position restraint gives "segmentation fault" for dt=0.030.

Please help me. I need to set a huge system with coarse grained methods. This is just the tutorial which I am not able to complete it successfully. please help.

Regards,
Naba

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9 years 2 months ago #741 by djurre
Replied by djurre on topic Problem in following MARTINI tutorial
Dear Naba,
As Xavier pointed out, there is likely a problem with the options in the mdp file. Below I'll give a minimalistic mdp file: It got everything to work and no more. You could use the same mdp file for a production run by changing the 'integrator' option to 'md'.

If it works, I would be interested which options gave the error.

Groetnis,
Djurre

MARTINI.mdp:

integrator = steep
dt = 0.030
nsteps = 100

nstlog = 1000
nstenergy = 500
nstxtcout = 500

nstlist = 10
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.4

coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
epsilon_rf = 1
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2

tcoupl = V-rescale
tc-grps = system
tau_t = 1.0
ref_t = 298
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 3.0
compressibility = 3e-4
ref_p = 1.0

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8 years 10 months ago #829 by jantunes
Replied by jantunes on topic Problem in following MARTINI tutorial

naba wrote: Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 3.5578291e+18
Maximum force = inf on atom 294
Norm of force = 1.0627526e+19


I had the same problem as Naba when doing tutorials 1a/1b (lipids), with energies around 1x10¹⁶, because only few minimization steps was made (around 15 too). And my way to get things right was to use "mdrun_d", a double precision one :)

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