[gmx-users] Negative pressure in NVT simulation

[Diana Lousa]

Hello,

Following this subject, if one wants to do a simulation with freeze groups
using the Verlet cutoff scheme in order to make efficient use of GPU
processing is it possible to use energy group exclusions? I tried it a
while ago (I am not sure if it was version 5.1 or 2016) and received an
error message saying that energy_grp_exclusions could not be used with the
Verlet schemce. If this is not possible how should one proceed to perform
simulations with freeze groups with the Verlet scheme?

Thanks in advance,

Best regards

Diana

On Sun, Jul 15, 2018 at 7:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/15/18 2:32 PM, Neda Rafiee wrote:
>
>> ;
>> energygrps          = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil
>> OGem OMB SIB SiSil SiGem HSil HGem OW HW
>> energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW
>> SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW
>> OGem OXB OW
>>
>> freezegrps          = SIB OXB OMB SiSil OSil SiGem OGem
>> freezedim           = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
>>
>
> You're not using energy group exclusions, which the manual recommends when
> freezing:
>
> "To avoid spurious contributions to the virial and pressure due to large
> forces between completely frozen atoms you need to use energy group
> exclusions, this also saves computing time."
>
> http://manual.gromacs.org/documentation/current/user-guide/
> mdp-options.html#non-equilibrium-md
>
> Freezing is a very severe artificial perturbation, so you will have to use
> hacks like that if you intend to do a simulation with so many things frozen.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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-- 
Diana Lousa
Post-doc
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal