Hello Sir, Can you please tell me how to couple ions with SOL ? Is there any command in gromacs to do that ?
Thanking you, Pawan On Tue, Apr 7, 2009 at 9:44 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > Pawan Kumar wrote: > >> 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 >> > > Don't couple ions seperately. See > http://wiki.gromacs.org/index.php/Thermostats > > Mark > > ; 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<mailto: >> 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 >> <mailto: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 >> <mailto: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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > _______________________________________________ > 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 >
_______________________________________________ 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
