Dear Mark, thank you for suggestions. I suspected that freezegrps does not work with NPT but I'm not sure that position restraints work with the same final effect. Concerning fixing the peptide on the simulation box, I would like to simulate as much as possible the fact that the peptide is fixed on a rigid support, so I'd like to avoid a peptide that rotates and fluctuates into the simulation box. I wonder if there is a way to fix the peptide like a handle in one of the walls of the box itself (obviously, in the internal part of the box). Thanks a lot to anybody will contribute to the discussion! Anna
Date: Thu, 19 May 2011 19:17:20 +1000 From: Mark Abraham <[email protected]> Subject: Re: [gmx-users] simulation of a peptide anchored to a support To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" On 19/05/2011 7:09 PM, Anna Marabotti wrote: > Dear gmx-users, > I would like to simulate the conformational behaviour of a peptide > covalently anchored to a rigid support with its N- and C-ter. I'm not > interested in simulating the support, so I wonder if there is a way to > simulate the peptide with its N- and C-ter fixed. Could freezegrps > work for this? Probably - but not with NPT. However, a strong position restraint is probably easier. > Otherwise (or in addition) could I fix the peptide on one side of the > simulation box, in order to avoid the fluctuation of the peptide into > the solvent? Not sure what you mean. > Finally, do I have to add special constraints/restraints to my molecule? Depends on the strategy. Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110519/2a8d564f/a ttachment-0001.html -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
