[gmx-users] Protein is Jumping from water Box

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed Apr 27 11:14:03 CEST 2016

Dear Abid,

I wouldn’t call it an issue nor an error. Your protein is still interacting with some periodic copy of the solvent molecules. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.

Kind regards,

On 27 Apr 2016, at 05:23, Abid Channa <abid_channa04 at yahoo.com<mailto:abid_channa04 at yahoo.com>> wrote:

Dear Gromacs users,
I have run 40 ns simulation , after 20 ns simulation my protein is continuously jumping from water Box. Is there any periodic boundary conditions issue with my system or an other error is that . Kindly give your valuable remarks.
Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
International Center for Chemical and Biological Sciences  (ICCBS),
University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. (309)
             Cell # +923013553051.
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