On 1/6/13 3:09 PM, Sanku M wrote:
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.
Use comm-mode = angular.
I am running the system using periodic boundary condition and using PME for
electrostatics.
You're certain to get periodicity artifacts. You should run without PBC and
with infinite cutoffs for nonbonded interactions to simulate the molecules in vacuo.
-Justin
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
Thanks
Sanku
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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