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?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, June 10, 2013 4:50 PM Subject: Re: [gmx-users] restraints on water oxygen atoms On 6/10/13 3:37 AM, Shima Arasteh wrote: > Thanks for your reply. > > The system I am trying to equilibrate is composed of popc/ > peptide/ions/water. I built the system by InflateGRO methodology as you wrote > in kalp-dppc tutorial. The last gro file which gave me the acceptable APL, > was used as the starting configuration in next steps. But before going on, I > found some overlaps between lipids acyl chains and peptide structure. So > tried to move the lipid residues caused the overlaps. Then there are some > gaps between peptide and near lipid chains. As a result, I see the water > cleavage in these regions. > Would you please give me any suggestions? How would I make a better packed > system without disturbing overlaps or crashes? > Would you please help me? > Don't manually delete lipids. InflateGRO overestimates APL, so if you reach your target value, realize that the lipids are more packed than that and the true APL is much smaller. I discuss that fact in the KALP-DPPC tutorial. I generally stop packing when the lipids claim to be about 10% higher than the desired APL. If you delete lipids because you've forced them together too much, then you're going to severely compromise the membrane. -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 -- 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
