Yeah! It is indeed a silly point to generate a velocity distribution at 0 K. ( Maxwell-Boltzmann will be in trouble) After the warm up, now let say my protein is in 300 K, can't I generate a velocity distribution at 300 k (using the keyword gen_vel = yes, gen_temp = 300 K gen_seed = 173529 ) during my production run?
Thanks, Tarak On Tue, Jun 4, 2013 at 10:10 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/4/13 12:17 PM, tarak karmakar 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 >> > > The introduction of constraints explains the observed behavior. You ran > an unconstrained simulation, then at step 0 of the constrained simulation, > the constraints have to be satisfied, which may introduce sudden movement > in atomic positions, hence large velocities and a high temperature. The > rule of thumb I always use - if you're going to use constraints during > production simulations, use constraints during equilibration. I have seen > several instances where unconstrained equilibration causes constrained > simulations to later fail. > > > 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? >> >> > That's an interesting question. If you're warming from 0 -> 300 K, I > don't know how grompp will generate velocities at 0 K, but regenerating > velocities after warming seems to defeat the purpose of doing the warming > at all, in my mind, since you're just going to re-randomize the entire > system by doing so. > > > -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
