[gmx-users] NPT simulation stage

[Swetha Srinivasan]

Hi Lemkul,

I am trying to simulate guanidium in water. My system contains 198 guanidium residues. But when I'm trying to use the grompp command ,I'm facing the problem of fudgeQQ, qi ,qj. I don't know what that means. I don't know how to rectify the error too. Plus if there are too many solvet molecules, how do I delete it ?

Thanks,

Swetha
________________________________________
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: Sunday, April 27, 2014 9:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] NPT simulation stage

On 4/27/14, 6:03 AM, Mahboobeh Eslami wrote:
>
>
> dear justin
> Thank you for your reply.
> My system is about 123,000 atoms and my box is cubic.
> I'm following conditions apply:
>
> pcoupl           = Parrinello-Rahman
> Pcoupltype       = Isotropic
> tau_p            = 0.5
> compressibility  = 4.5e-5
> ref_p            = 1.0
> refcoord_scaling = com
>
> But the average pressure is not good repeatability.
>
> To fix this problem I did two NPT simulation stage
> The first 100ps by brendsand barostat then 100ps by Parrinello-Rahman
> barostatbut Still not good repeatability. I frequently change tau_p but I did
> not get any results. Increase the NPT simulation time did not solve the problem.
> I strongly need your help
> Thank you sincerely for your kindness

What I was asking for previously were the actual results - i.e. what values of
pressure you achieved.  Please provide the exact g_energy output.

When you increased the time, how long were the new runs?  100 ps is fairly short
for any NPT process.  Some systems may take a few ns to converge, depending on
what their contents are.

-Justin

> On Friday, April 25, 2014 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote:
>  > hi GMX users
>  > please help me
>  > i want to simulate protein-ligand complex by gromacs4.6.5
>  > when i repeat NPT simulation stage  many times,  simulation results are very
> different for the pressure average.I sincerely thank you for your guidance
>
>  >
>
> Pressure is probably the most ill-defined quantity in MD simulations.  It can
> fluctuate dramatically.  Without the actual numbers, it's hard to comment, but
> issues related to pressure have been discussed extensively over the list in the
> past and there is useful information in
> http://www.gromacs.org/Documentation/Terminology/Pressure.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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