[gmx-users] Simulation in vacuum

Sun Jan 22 11:24:14 CET 2017

Hi,

Like the messages say, you can only use the Verlet scheme with periodic
systems. Use the group scheme.

Mark

On Sun, 22 Jan 2017 06:54 Мижээ Батсайхан <b.mijiddorj at gmail.com> wrote:

> 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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