[gmx-users] Pressure problem in EM simulation

Mark Abraham mark.j.abraham at gmail.com
Sun Mar 19 02:23:29 CET 2017

```Hi,

You haven't done a simulation, you've moved down a potential energy surface
from one point to another. Of course the potential energy deviates. How
much depends how far away from something reasonable you were when you
started :-)

Mark

On Sun, Mar 19, 2017 at 2:19 AM Mishelle Oña <samimishu at hotmail.com> wrote:

>
> Another question for the same simulation. I got this values of potential
> energy:
>
> Average> -127776
>
> Err.Est.>4900
>
> RMSD>12891.3
>
> Tot-Drift> -32877.9
>
> I think the RMSD is way too high. What do you think?
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> Lemkul <jalemkul at vt.edu>
> Sent: Saturday, March 18, 2017 8:06 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Pressure problem in EM simulation
>
>
>
> On 3/18/17 9:00 PM, Mishelle Oña wrote:
> > Hello!
> >
> > I have a question about pressure in EM simulation. I am using Steepest
> descent method in a water polymer system. My pressure gets this value:
> >
> > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> >
> -------------------------------------------------------------------------------
> > Pressure                   -2843.38         65    162.655   -446.059
> (bar)
> >
> > The pressure value is very weird. Is this normal? or I am doing
> something wrong?
> >
>
> There's no barostat or velocities during EM so the value you see has no
> real
> significance.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<
> http://mackerell.umaryland.edu/~jalemkul>
>
> Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul>
> mackerell.umaryland.edu
>
>
>
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