I can be used Gromacs programs and Gromos96 for molecular dynamics simulations of protein-ligand complexes .
After 10 nanoseconds of 20 nanoseconds of time that we have Obtain an unusual RMSD, comes in your opinion, what is wrong?
Parameters that will be used are as follows:
title = Protein-ligand complex MD simulation
; Run parameters
integrator = md
nsteps = 10000000
dt = 0.002
; Output control
nstxout = 0
nstvout = 0
nstenergy = 1000
nstlog = 1000
nstxtcout = 1000
energygrps = system
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
; Temperature coupling
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Pressure coupling
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = no
This is a clear periodicity effect. Your protein is jumping back and forth between periodic images. Proper re-centering with trjconv will solve it. Some Gromacs tools deal well with PBC, g_rms does not. This is a common problem.
This is a clear periodicity effect. Your protein is jumping back and forth between periodic images. Proper re-centering with trjconv will solve it. Some Gromacs tools deal well with PBC, g_rms does not. This is a common problem.
I know this is a bit late, but you may want to try the 'autoimage' command in CPPTRAJ (freely available with AmberTools 14), which was designed to simplify the re-imaging of trajectories. CPPTRAJ should work fine with Gromacs trajectories.
Dear Javad,
I am facing same type of problem in my MDS also. I used same force field for protein ligand simulation. Please suggest me command if you solved this problem. Please help me. I am so confuse.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics