[gmx-users] Simulation in vacuum

[Мижээ Батсайхан]

Dear Erik,

Thank you very much for your kind reply.

Best regards,

Mijiddorj


>
> ------------------------------
>
> Message: 3
> Date: Fri, 20 Jan 2017 19:01:10 +0900
> From: ????? ?????????   <b.mijiddorj at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Simulation in vacuum
> Message-ID:
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> Content-Type: text/plain; charset=UTF-8
>
> 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
>
>
> ------------------------------
>
> 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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