Hi Syma I think that Gromacs applies a neutralising charge distribution if there is a charged system.
Best wishes George Dr. George Patargias Polymer IRC Group University of Leeds Leeds, LS2 9JT, UK -----Original Message----- From: [EMAIL PROTECTED] on behalf of Syma Khalid Sent: Tue 10/30/2007 5:30 PM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] langevin dynamics Hi Mark, Firstly, thanks for your prompt response. If they really are just counter-ions, then simple electrostatics will do that... this is a side-issue, however. Please can you explain the above? Will the ions simply collapse onto my protein? The counter ions are simply to there to give me an overall neutral system. Is there some other way I can get a neutral system? Many thanks, -Syma *********************************************************************** Dr Syma Khalid RCUK Fellow (Chemical Biology) School of Chemistry University of Southampton Highfield Southampton phone: (0)2380-594176 SO17 1BJ email: [EMAIL PROTECTED] U.K. *********************************************************************** -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: 30 October 2007 17:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] langevin dynamics Syma Khalid wrote: > Dear all, > > > > I was wondering if someone could offer some advice? > > I would like to run an atomistic langevin dynamics simulation (as I > don't want to include water explicitly). If I add the appropriate > langevin dynamics options in the mdp file, then is there any reason why > I shouldn't use explicit counter ions (unfortunately my protein has an > overall charge)? In what medium are they going to move? How realistic is that going to be? > Obviously I would use periodic boundary conditions so the ions don't > wander off. If they really are just counter-ions, then simple electrostatics will do that... this is a side-issue, however. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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