[gmx-users] Simulation in vacuum

[Erik Marklund]

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 Skłodowska 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, Мижээ Батсайхан <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
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.