I am not sure whether a pressure coupling equilibration enlarges the specified box size of the simulation :) if the box size is not appropriate to maintain the pressure coupling the simulation probably blow up instead of adjusting the box size to a bigger one.
For more info check the following links and consult with gromacs manual http://www.gromacs.org/Documentation/Terminology/Equilibration?highlight=equilibration http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling Cheers, EB -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Tuesday, 14 August 2012 6:08 PM To: Discussion list for GROMACS users Subject: [gmx-users] Fw: box of simulation Hi Emanuel, Thank you very much from your response. yes, my topology is correct. It means that it isn't one problem and it is natural.yes? This question is because of in the most of papers has been said that the box is enlarged with equilibrium but my box become smaller! Best Regards Sara ----- Original Message ----- From: Emanuel Birru <emanuel.bi...@monash.edu> To: 'mohammad agha' <mra...@yahoo.com>; 'Discussion list for GROMACS users' <gmx-users@gromacs.org> Cc: Sent: Tuesday, August 14, 2012 12:06 PM Subject: RE: [gmx-users] box of simulation Hi Sara, The number of molecules in your .gro file and .top file should be the same. That means when you want to add 12000 solvent molecules, change the number of solvent molecules in your topology file to 12000. The total number of your solvent and solute molecules in you topology and coordinate files should be the same. When you do constant pressure equilibration it is normal to see your box shrinking as long as you are pretty sure that the number of molecules in the box is correct. I you do need no change on the size of the box, run a constant volume equilibration. Cheers, EB -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Tuesday, 14 August 2012 5:27 PM To: Discussion list for GROMACS users Subject: [gmx-users] box of simulation Dear Gromacs Users: When I want to place 12000 solvent molecule in the box (15*15*15) it say: number of coordinates in coordinate file (ctacyc.gro, 28794) does not match topology (topol.top, 37950) it means that I should enlarge the box to place all of solvent molecules into that. But when the system equilibrium with running pr.mdp, box become smaller till 13.9*13.9*13.9!!! What should I do with this problem? Is it a problem?! Thank you very muchin advance. Best Regards Sara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
