On 3/18/17 9:18 PM, Mishelle Oña wrote:
Thanks for your answer Justin.
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?
Consider the name "energy minimization" and then plot the energy as a function
of step. Does it make sense to try to obtain average statistics during a
process designed to dramatically alter the energy?
-Justin
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul
<jalem...@vt.edu>
Sent: Saturday, March 18, 2017 8:06 PM
To: gmx-us...@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
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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
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Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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