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
