Would you please tell me which initial deletion radius? And do you mean a smaller scale up factor ( for example 0.90 ) by saying shrink more slowly?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, June 10, 2013 8:22 PM Subject: Re: [gmx-users] restraints on water oxygen atoms On 6/10/13 11:44 AM, Shima Arasteh wrote: > Thanks for your reply. > When I look into the earlier gro file ( with APL even higher than 10% of > desired APL), I still see some lipid residues in improper places, forexample > in phenyl rings. How can I go on with it? If I choose the gro file without > any overlap, the APL becomes very high and it would not be acceptable. > Do you still suggest not to delete lipids manually? > I don't see how that's possible, quite honestly. If the initial deletion radius was sufficient, then lipid molecules shouldn't force their way through phenyl rings - the forces required would be astronomical. I don't have any details of your protocol, so it's hard to comment further. If things are getting jammed together this badly, you should probably be shrinking more slowly than you currently are. I never advocate for manual deletion of lipids, because, as you can see from experience, doing so creates a world of problems during equilibration. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
