This is the input file for equilibration.
title = NVT Equilibration
; Run parameters
integrator = sd ; leap-frog integrator
nsteps = 250000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 5000 ; save coordinates every 10 ps
nstvout = 5000 ; save velocities every 10 ps
nstenergy = 5000 ; save energies every 10 ps
nstlog = 5000 ; update log file every 10 ps
; Bond parameters
continuation = no ; Initial simulation
constraint_algorithm = lincs
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
coulombtype = cut-off
nstlist = 5 ; 10 fs
rlist = 0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
rvdw = 0 ; short-range van der Waals cutoff (in nm)
rgbradii = 0
; Temperature coupling is on
tcoupl = V-rescale ; Weak coupling for initial equilibration
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 298 ; reference temperature, one for each group, in K
;gen_vel = yes ; Velocity generation is on
gen_temp = 10 ; temperature for velocity generation
gen_seed = -1 ; random seed
; COM motion removal
; These options remove COM motion of the system
;nstcomm = 10
comm-mode = Linear
comm-grps = System
pbc = no
cut-off_scheme = Group
implicit_solvent = GBSA
gb_algorithm = OBC
I setted nstlist>0 because domain decomposition is not supported at nstlist=0.
Using Simple algorithm for neighbor seach I was getting following error: "segmentation fault (core dumped)". (rlist=rvdw=rcoloumb=0)
While when I was using "grid" for neighbor search I was getting "Atom moved too far" there I was using a rlist=rvdw=rcoloumb=1.4.
There is something inherently unstable about your system. Infinite cutoffs are correct for implicit solvent and should not be changed. Make sure your previous energy minimization was adequate and perhaps attempt to prepare an explicit solvent simulation or in vacuo MD run to test.
Please note that the implicit solvent code in GROMACS is no longer supported and is not highly optimized for performance.
1. System is minimised in avogadro first and then it was submitted for minimisation in gromacs 2018. This way l am getting negative energy (using steepest decent algorithm). System has -6*10^4 kj/mol energy after minimisation in implicit solvent.
2. Simulation of the same system is already running in explicit solvent (potential energy after minimisation=-1.5*10^6kj/mol). But there size is a constraint.
That's why I am trying to set simulation in Implicit solvent.
3. Also, I want to run REMD in implicit solvent.
Again I will emphasize that the implicit solvent code in GROMACS was never well tested and that motivated its removal. You should not use version 2018 and then try to move back to 4.5 or whatever version you're using that supports implicit solvent. Use the same version to make sure your workflow works.
I do not know if implicit + REMD will work. Likely the compatibility of those codes was never tested. You're better off using a more robust and highly optimized code like AMBER for this kind of simulation.
Amit Kumar Dear Amit hi
could you solve your problem in using REMD simulation with implicit solvent in Gromacs?
I confront with the same problems.
Could you please help me if you have done this simulation?
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