Respected Sir, Greetings from Pawan. Sorry for the inconvenience about the .mdp file. The mdp file used for the final run is * final.mdp file**
*title = Protein in POPC bilayer cpp = /usr/bin/cpp constraints = all-bonds constraint-algorithm= Lincs integrator = md dt = 0.002 nsteps = 5000 nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 vdw-type = Cut-off rvdw = 1 ; Berendsen temperature coupling is on in two groups tcoupl = berendsen tc_grps = Protein POPC SOL CL- tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 ; Energy monitoring energygrps = Protein POPC SOL CL- ; Pressure coupling is on ;Pcoupl = berendsen tau_p = 2.0 2.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 Pcoupl_type = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 * mdp file for position restraint mdrun* title = Protein in POPC bilayer cpp = /usr/bin/cpp define = -DPOSRES -DPOSRES_LIPID constraints = all-bonds constraint-algorithm= Lincs integrator = md dt = 0.002 nsteps = 5000 nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 vdw-type = Cut-off rvdw = 1 ; Berendsen temperature coupling is on in two groups tcoupl = berendsen tc_grps = Protein POPC SOL CL- tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 ; Energy monitoring energygrps = Protein POPC SOL CL- ; Pressure coupling is on ;Pcoupl = berendsen tau_p = 2.0 2.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 Pcoupl_type = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Thanking you, Yours sincerely, Pawan On Mon, Apr 6, 2009 at 5:35 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Pawan Kumar wrote: > >> >> Respected Sir, >> >> Greetings from Pawan. >> >> 1. Were there gaps between the water and lipid headgroups? If so, >> the lipids may be pulling towards the solvent. Restrain the lipids >> and run an equilibration for a longer time. >> >> Gap was there when I used a value of 0.5 in the vdwradii.dat file. The >> gap reduced as I decreased the value from 0.5 to 0.35 to the default of >> 0.15. I tried all the three possibilities. >> When I used the default vdwradii.dat file and made the solvation followed >> by simulation runs the lipids didnt pull apart. But there were water >> molecules on the sides of the bilayer and not in the interior. >> >> > > This indicates to me that the gaps are causing the problem. Do not run > simulations with water in or around the lipids; it is not realistic. You > can clean up such a starting structure, either by some clever script like > those on the wiki, or by looking at the structure, taking note of which > water molecules are offending, and deleting them manually from the > coordinate file. > > The other option is to temporarily give genbox a box that is slightly > smaller in the x-y dimensions, so that it will try to place less water > around the POPC periphery. > > >> 2. 5000 steps is far too short to expect any realistic behavior for >> lipids. Equilibration can take upwards of 10-20 ns. >> >> As per your suggestion I have made the final mdrun now again with 500000 >> steps. Hopefully this will work. >> >> >> 3. You haven't mentioned the contents of your .mdp file. Maybe >> you're doing something wrong. >> >> I am using the same .mdp file which I posted before. I have just removed >> the restraints. >> >> > I don't have record of the previous email; as a general guide, post the > .mdp by default when experiencing weird behavior. That way the users on > this list won't have to go combing through the archive to find it. If you > want free help, make it easy to help you :) > > -Justin > > >> 4. Are you using Gromos/Berger or OPLS/converted Berger for your >> system? There have been so many of these questions from different >> users over the last few days that it's hard to keep track. If you >> are using OPLS/converted Berger you may have made a mistake in >> translating the C6/C12 parameters. >> >> I am using gromos 96 force field (G43a1) and as per your suggestion I >> have edited the lipid.itp file to remove the part containing " lipid-gromos >> interactions". >> >> >> >> Thanking you, >> >> Yours sincerely, >> Pawan >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > 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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