[gmx-users] negative pressures!
Mungikar, Amol Arvind (UMR-Student)
mungikar at umr.edu
Fri Feb 20 06:00:02 CET 2004
This time i ran 'spc216.gro' given in the 'tutor' folder of the gromacs package ... without changing a single line ... and again the same problem .... do you think that my installation is a problem, maybe the random number generator is not working properly. I am using a linux machine, I had some problems previously with the random number generator with this machine while using Monte Carlo simulations (my own code). But, its almost difficult with Gromacs to check that. Can you suggest me something?
I am really sorry to bother again and again on this one.
Thanks for your time.
From: gmx-users-admin at gromacs.org on behalf of David van der Spoel
Sent: Thu 2/19/2004 12:12 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] negative pressures!
On Thu, 19 Feb 2004, Mungikar, Amol Arvind (UMR-Student) wrote:
>I posted a similar message few days back, and since then I am trying to find out where the bug is! I ran NVT md simulations for water, peptide-water. And everytime for this NVT ensemble run, I am getting pressures +/- 1000 bars. Dr.Spoel mentioned that this might be because of a 'air bubble' in the system, or based on previous discussions in this forum it maybe due to the high (wrong) densities. I checked the density value (1 gm/cm3) for water box several times. I checked all the RDFs but i couldnt locate anything wrong here. I am sure that I am missing out something, but sadly i dont know what. Kindly help me out in this matter.Thank you very much in advance.
depending on your cut/off treatment, but for SPC the equilibrium density
is roughly 977 g/l. If you have 1000 g/l you'll have positive pressure.
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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