[gmx-users] negative pressures!

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 19 19:13:01 CET 2004

On Thu, 19 Feb 2004, Mungikar, Amol Arvind (UMR-Student) wrote:

>Dear all,
>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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