Respected Sir, Greetings from Pawan. Thanks for your reply. After the position restraint mdrun the system looked quite justified as I restrained both the protein and the lipids. Is it because of the lesser number of steps ? I use 5000 steps with dt value of 0.002.
Thanking you, Pawan On Mon, Apr 6, 2009 at 1:11 PM, Kukol, Andreas <a.ku...@herts.ac.uk> wrote: > Apparently the final mdrun has not worked successfully. It would be > interesting to see what the system looks like after the position restraint > mdrun. > > Andreas > > >>>>>>>>>>> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Pawan Kumar > Sent: 06 April 2009 07:47 > To: Discussion list for GROMACS users; jalem...@vt.edu > Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer > > Respected Sir, > > Greetings from Pawan. > Thanks for all your suggestions and help. > The solvation is completed and the system is neutralized. > The position restraint mdrun and final mdrun has worked out successfully > without any warnings and errors this time. > The structure after the final mdrun is not quite acceptable as the lipids > have pulled apart and there is a huge gap between the two layers of the > lipids. I have made the run for 5000 steps with dt = 0.002. > Any suggestions please. > > Thanking you, > > Yours sincerely, > Pawan > On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Pawan Kumar wrote: > Respected Sir, > > Greetings from Pawan. > Thanks for all your kind help and suggestions. > I will work on this and ask you if I have further doubts. > Is it fine if I use the perl code given in > wiki.gromacs.org/membrane-simulations < > http://wiki.gromacs.org/membrane-simulations> for solvation after the > genbox step to remove extra waters from the hydrophobic part of the bilayer > ? > > You mean the C program or shell script at > http://wiki.gromacs.org/index.php/Membrane_Simulations? Yes, either of > those should be fine. > > -Justin > Thanking you, > > Yours sincerely, > Pawan > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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://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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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