[gmx-users] Simulation in vacuum

Sun Jan 22 06:53:53 CET 2017

Dear Erik,

Thank you very much for helping me.
I have got 2 errors from grompp using gromacs v5.1.

ERROR 1 [file nve.mdp]:
  With Verlet lists only full pbc or pbc=xy with walls is supported

ERROR 2 [file nve.mdp]:
  With Verlet lists nstlist should be larger than 0

How can I fix these? I copied my mdp file.

#############################################
title       = NVE equilibration
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 100000000      ; 1 * 100000000 fs= 100000 ps = 100 ns
dt          = 0.001     ; 1 fs
; mode for center of mass motion removal
comm-mode                = Angular

; Output control
nstxout     = 5000
nstvout     = 5000
nstenergy   = 5000
nstlog      = 500
;energygrps  =

; Bond parameters
continuation    = no
constraint_algorithm = lincs
constraints     = hbonds
lincs_iter      = 2
lincs_order     = 4

; Neighborsearching PARAMETERS
vdw-type    = cut-off
verlet-buffer-tolerance = -1
rlist         = 1
nstlist     = 0
ns_type     = grid
pbc         = no

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = cut-off
rcoulomb-switch          = 0
rcoulomb                 = 0.0
rvdw                     = 0.0
rvdw-switch              = 0.0
fourierspacing           = 0.16
epsilon_r                = 1
epsilon_rf               = 78
; EWALD/PME/PPPM parameters
pme_order                = 4          ; cubic interpolation

; Temperature coupling
tcoupl      = no
;tc-grps     =
;tau_t       = 0.1
;ref_t       = 300
; Pressure coupling
pcoupl      = no        ; no pressure coupling in NVT
; Dispersion correction
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1       ; generate a random seed
################################################################

Best regards,
Mijiddorj

> ------------------------------
> >
> > Message: 4
> > Date: Fri, 20 Jan 2017 10:30:59 +0000
> > From: Erik Marklund <erik.marklund at kemi.uu.se>
> > To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] Simulation in vacuum
> > Message-ID: <7745284C-EA36-4189-80A6-0A6AB4986FDC at kemi.uu.se>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Mijiddorj,
> >
> > We have had good energy conservation with bond constraints and a 1 fs
> time
> > step under double precision, using a setup similar to yours. We did not
> > remove rotation however, because we wanted to honour the rotational
> > temperature of the system. Whether that is an important choice or not is
> > for you to decide, but do note that the spinning ice cube effect is an
> > artefact arising from the thermostat, which is turned off in your setup.
> >
> > Whether bonds should be constrained or not is related to what your
> > scientific questions are, and the time step depends on what bonds are
> > constrained, if any. I can?t remember what LINCS parameters we used, but
> be
> > prepared to increase the order and/or iter. Consult the manual for
> details.
> >
> > Kind regards,
> > Erik
> >
> > ______________________________
> > Erik Marklund, PhD
> > Marie Sk?odowska Curie INCA Fellow
> > Department of Chemistry ? BMC
> > Uppsala Universtity
> > erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>
> >
> > On 20 Jan 2017, at 11:01, ????? ????????? <b.mijiddorj at gmail.com<mailto:
> > b.mijiddorj at gmail.com>> wrote:
> >
> > Dear gmx users,
> >
> > I would like to get experience of simulation in vacuum. Please suggest me
> > tutorials, and advice me.
> >
> > I read about following comments which written on Shourjiya Sanyal
> tutorial.
> > Can you discuss about it?
> >
> > In vacuum simulation, integration should be reduced compared to solvent
> > phase simulation. Periodic boundary conditions, non-bonded interaction
> > cutoffs, temperature coupling and pressure coupling were all turned off.
> > Center of mass translation and rotation around the center of mass are to
> be
> > removed to avoid the fast spin of the protein. One should also constrain
> > the hydrogen bond using algorithms like SHAKE/LINCS.
> >
> > http://www.shourjya.thinkbiosolution.com/md-
> simulation-in-gas-phasevacuum-
> > with-gromacs/
> >
> >
> > Best regards,
> > Mijiddorj
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