- Posts: 1
Problem in following MARTINI tutorial
- naba
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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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- xavier
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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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- djurre
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- Admin
- Posts: 272
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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- jantunes
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- Posts: 10
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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