[gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 16 17:13:51 CEST 2018 

Hi,

No idea sorry. I never attempt anything like this, in part because frozen
groups are anyway unphysical.

Mark

On Mon, Jul 16, 2018 at 2:56 PM Neda Rafiee <nerafiee at ipm.ir> wrote:

> Dear Mark,
> I removed different residues from my energy group list, but still the
> problem of very large negative pressure exist. Any other solution?
> Thanks in advance.
> Neda
>
>
> ----- Original Message -----
> From: Neda Rafiee <nerafiee at ipm.ir>
> To: gmx-users at gromacs.org
> Sent: Mon, 16 Jul 2018 12:03:34 +0430 (IRDT)
> Subject: Re: [gmx-users]        [Spam-FG]
>  [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
>
> Dear Mark,
> Thanks a lot for your useful suggestions
> Neda
>
>
> ----- Original Message -----
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Sent: Mon, 16 Jul 2018 11:49:38 +0430 (IRDT)
> Subject: Re: [gmx-users] [Spam-FG]
> [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
>
> Hi,
>
> I presume that's because you still have interactions between groups that
> are frozen.
>
> You can make your life easier by using only the groups you need for your
> simulation, e.g. those needing a table and those that are frozen. If you
> are trying to get per-residue decomposition, then (first) make sure your
> force field was parametrized such that this is meaningful (most aren't),
> and prefer to do that analysis using mdrun -rerun. mdrun goes slower for
> each energy group that has interactions to compute, so minimize that.
>
> I would also have done a simulation with just my slab and found this
> pressure issue back then. It is good practice to add complexity to models
> incrementally, after validating your expectations on the simulation at the
> previous stage.
>
> Mark
>
> On Mon, Jul 16, 2018 at 9:07 AM Neda Rafiee <nerafiee at ipm.ir> wrote:
>
> > Dear Justin,
> > I added the following energy exclusion pairs to my mdp file. Now
> potential
> > energy decreased significantly but still I have a very large negative
> > pressure (minus 10 to power 28) in my system. It seems that pressure is
> the
> > same as before.Should I do anything else?
> >
> > energygrp-excl= SIB SIB  SIB OXB  SIB OMB  SIB SiSil  SIB OSil  SIB SiGem
> > SIB OGem  OXB OXB  OXB OMB  OXB SiSil  OXB OSil  OXB SiGem  OXB OGem  OMB
> > OMB  OMB SiSil  OMB OSil  OMB SiGem  OMB OGem  SiSil SiSil  SiSil OSil
> > SiSil SiGem  SiSil OGem  OSil OSil  OSil SiGem  OSil OGem  SiGem SiGem
> > SiGem OGem  OGem OGem
> >
> > Thanks
> > Neda
> >
> > ----- Original Message -----
> > From: Neda Rafiee <nerafiee at ipm.ir>
> > To: gmx-users at gromacs.org
> > Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT)
> > Subject: [Spam-FG][gmx-users]
> > [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
> >
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> >
> > <PRE>
> > Dear Justin,
> > Thanks a lot for your response.
> > Neda
> >
> > ----- Original Message -----
> > From: Justin Lemkul
> > To: gmx-users at gromacs.org
> > Sent: Sun, 15 Jul 2018 23:09:11 +0430 (IRDT)
> > Subject: [Spam-FG] Re: [gmx-users] Negative pressure in NVT simulation
> >
> >
> >
> > <DIV><a style="color: blue; background-color: ffffdd" href="
> > http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWARoweXYADkhffkN1
> >
> >
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> > If this email is not spam, click here to submit the signatures to
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> > </a></DIV>
> > <PRE>
> > On 7/15/18 2:32 PM, Neda Rafiee wrote:
> > &gt; ;
> > &gt; energygrps          = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB
> > OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW
> > &gt; 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
> > &gt;
> > &gt; freezegrps          = SIB OXB OMB SiSil OSil SiGem OGem
> > &gt; freezedim           = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
> >
> > You&#39;re not using energy group exclusions, which the manual recommends
> > when freezing:
> >
> > &quot;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.&quot;
> >
> >
> >
> 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 thin
> <https://maps.google.com/?q=tend+to+do+a+simulation+with+so+many+thin&entry=gmail&source=g>
> gs
> > 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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