I'm extremely sorry for copying the other '.mdp' file here. This is the modified one I just created after seeing your reply. In the previous case I didn't use 'continuation'.
On Tue, Jun 4, 2013 at 9:47 PM, tarak karmakar <tarak20...@gmail.com> wrote: > Thanks Justin. > Sorry for not uploading the full .mdp. Here it is, > > ; 7.3.3 Run Control > integrator = md > tinit = 0 > dt = 0.001 > nsteps = 5000000 > nstcomm = 1 > comm_grps = system > comm_mode = linear > energygrps = system > > ; 7.3.8 Output Control > nstxout = 5000 > nstfout = 5000 > nstlog = 1000 > nstenergy = 1000 > nstxtcout = 1000 > xtc_precision = 1000 > xtc_grps = System > > ; 7.3.9 Neighbor Searching > nstlist = 10 > ns_type = grid > pbc = xyz > rlist = 1.2 > rlistlong = 1.4 > > ; 7.3.10 Electrostatics > coulombtype = PME > rcoulomb = 1.2 > fourierspacing = 0.12 > pme_order = 4 > ewald_rtol = 1e-5 > > ; 7.3.11 VdW > vdwtype = switch > rvdw = 1.2 > rvdw-switch = 1.0 > > DispCorr = Ener > > > ; 7.3.14 Temperature Coupling > tcoupl = nose-hoover > tc_grps = system > tau_t = 1.0 > ref_t = 300 > > ; 7.3.15 Pressure Coupling > pcoupl = parrinello-rahman > pcoupltype = isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > > gen_vel = yes > gen_temp = 300 > gen_seed = 93873959697 > > ; 7.3.18 Bonds > constraints = h-bonds > constraint_algorithm = LINCS > continuation = yes > lincs_order = 4 > lincs_iter = 1 > lincs_warnangle = 30 > > Note: Using CHARMM27 force field > > I didn't use the 'continuation' part here. > In the heating run I didn't put any constraints but in the production MD, > I do apply constraints to the covalent bonds involving hydrogens. I just > want to test the ligand movement inside the protein cavity in different set > of initial velocities to get the feelings of how ligand is interacting with > certain residues. > So, then should I use these different velocity generating seeds during the > warm up step? > > Thanks, > Tarak > > > > > > > > On Tue, Jun 4, 2013 at 5:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 6/4/13 8:07 AM, tarak karmakar wrote: >> >>> Dear All, >>> >>> Although I have set gen_temp = 300, it is showing the initial temperature >>> 445.7 K, generated at the very beginning of the run. >>> >>> gen_vel = yes ; velocity generation >>> gen_temp = 300 >>> gen_seed = 93873959697 >>> >>> Is it because of a bad geometry? In mailing list I came across this >>> thread >>> [ >>> http://comments.gmane.org/**gmane.science.biology.gromacs.**user/41931<http://comments.gmane.org/gmane.science.biology.gromacs.user/41931> >>> ] >>> Prior to this production run, I heated my system slowly from 0 K to 300 K >>> within 300 ps time span. >>> It would be very helpful if someone suggests me the way to deal with this >>> problem? >>> >>> >> A full .mdp file is always more useful than a small snippet. I have seen >> this same behavior when the "continuation" parameter is incorrectly set - >> have you used "continuation = yes" in your .mdp file? If not, the >> constraints get messed up and your initial velocities can get all messed up. >> >> A larger point is this - why are you re-generating velocities after >> heating the system from 0 to 300 K? Why not simply preserve the ensemble >> at 300 K by using a .cpt file? >> >> -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<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
