[gmx-users] Pressure calculated from g_energy showing negative value

[Eric Jakobsson]

In a small box you will always get very large pressure fluctuations, 
especially if you look at very small time increments.  There is no physical 
reason why the virial (and hence the computed pressure), should not be 
negative at any instant.

Eric

At 11:42 AM 10/27/2003 -0600, you wrote:
>Dear gmx-users,
>
>In the .mdp file I have included following parameters for pressure
>coupling.
>
>pcoupl                            = berendsen
>tau_p                             = 0.5
>compressibility                   = 4.5e-5
>ref_p                             = 1.0
>
> >From g_energy calculation I got negative value of pressure with large
>fluctuation. What could be the  reason for this ?
>
>
>The presure vs time  plot I have send as an attachment.
>
>The following is the output which I got after the g_energy calculation of
>pressure.
>
>Statistics over 500001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets
>
>Energy                      Average       RMSD     Fluct.      Drift
>Tot-Drift
>-------------------------------------------------------------------------------
>Pressure (bar)              1.01185    161.177    161.176 0.00204041
>2.04041
>
>I will grateful if  anyone explains its reason.
>
>regards,
>Sunita Patel
>
>
>
>-------------------------------------------------------------------------------
>Sunita Patel
>Biophysical Lab.,
>Dept. of Chemistry,
>Indian Institute of Technology(IIT) Bombay,
>Powai, Mumbai, Maharashtra,
>INDIA-400076.
>
>Tel: (91)-22-25764176.
>Email:sunita at chem.iitb.ac.in
>-------------------------------------------------------------------------------
>
>

---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

(Currently on leave to NIH to serve as Director of Center for 
Bioinformatics and Computational Biology at the National Institute of 
General Medical Sciences and Chair of the NIH Biomedical Information 
Science and Technology Initiative Consortium.  Usual schedule is four days 
a week at NIH and three days a week at Illlinois.)