GROMACS version: 2024.4
GROMACS modification: Yes/No
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Martini 3
Hello,
I made three replicates of a membrane and equillibrated them and ran for production
Then I added proteins (AMPs) to these production files. I need to add a frozen water layer (FW) to one side of my membrane to stop the AMPs from interacting with both sides of the membrane.
I needed to put position restraints on one layer of water to make the FW.
Two of my replicates ran for minimization and equillibration perfectly without error and now are running for production.
When I looked at one of the reps on VMD at the end of the equilibration, I realized that it has position restraints on everything, water, membrane, AMPs, FW…
All the mdp and itp files are also the same which confused me because it worked for all of the other 2 reps.
It is important to mention that I only wanted the POSRES for equillibration and production and not minimization. so the emin.mdp doesn’t define POSRES anyways. I am confused that maybe this problem arises from somewhere else.
But interestingly, when I looked at my log files for minimization, I realized that it only was done in 89 steps while it took the other reps over 300 or 800 steps to finish.
I also checked my other itps to make sure ifdef POSRES is not defined and none of them had it.
problematic rep log:
Steepest Descents converged to Fmax < 500 in 82 steps
Potential Energy = -6.0585990e+06
Maximum force = 3.0067920e+02 on atom 72176
Norm of force = 3.6262449e+01
Healthy rep log:
Steepest Descents converged to Fmax < 500 in 871 steps
Potential Energy = -7.3980540e+06
Maximum force = 4.5027390e+02 on atom 55664
Norm of force = 5.9344858e+00
Healthy rep2 log:
Steepest Descents converged to Fmax < 500 in 335 steps
Potential Energy = -7.0537610e+06
Maximum force = 4.7208441e+02 on atom 168219
Norm of force = 1.1086542e+01
I have my FW.itp and mdp posted below:
FW.itp:
[ moleculetype ]
; molname nrexcl
FW 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 FW 1 FW FW 1 0
[position-restraints]
#ifdef POSRES
1 1 100000 100000 100000
emin.mdp:
title = Martini
integrator = steep
nsteps = 1000000
nstcomm = 100
emtol = 500
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 100
compressed-x-grps =
energygrps = system
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
constraints = none
constraint_algorithm = Lincs
lincs_iter = 8
lincs_order = 16