[gmx-users] simulating protein in gas-phase

Sanku M msanku65 at yahoo.com
Sun Jan 6 21:09:41 CET 2013

Dear Gromacs users,
  I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and ligand in gas phase.
I have previously run the simulation in water without any problem. Now, I want to compare the result to see the effect of solvent.

But for running the same simulation after stripping the waters from the simulation box I am looking for some advise.
I am having following issues:
a) If I use 'md' i.e usual leap frog integrator with nstcomm=10 and comm-mode=Linear( this was the setup I had when I ran the simulation in water), I find after running the system of protein and ligand in gas phase for some time ( about 1 ns ), the protein starts rotating i.e it generates a very high angular momentum.
b) So, I thought of using comm-mode=angular,,, But then grompp gives me a warning that removing rotation is not a problem only if I have only 1 molecule in the system ...which is not the case here as I have ligand and some ions . Any suggestion is highly appreciated. I can change nstcomm=1 using comm-mode=Linear but I am not sure it will stop the rotation of the protein about its own axis.
I am running the system using periodic boundary condition and using PME for electrostatics.

c) another option I thought of was using 'sd' integrator but considering my simulation in water having been performed using md integrator, I was looking to keep my .mdp file option as similar as possible in both cases.

Any help on how to perform the simulations in gas-phase will be highly appreciated.

Here is my current .mdp options:
title       = Umbrella pulling simulation
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 1500000     ; 800 ps
nstcomm     = 10
; Output parameters
nstxout     = 0000      ; every 10 ps
nstvout     = 0000
nstfout     = 0000
nstxtcout   = 250
nstenergy   = 250
; Bond parameters
constraint_algorithm    = lincs
constraints             = hbonds
continuation            = yes
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid
rlist       = 1.4
rcoulomb    = 1.4
rvdw        = 1.4
; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl      = Nose-Hoover
tc_grps     =  System
tau_t       = 0.5
ref_t       = 300
; Pressure coupling is on
Pcoupl          = no
pcoupltype      = isotropic
tau_p           = 1.0
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocities is on
gen_vel     =  yes
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres


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