On Wed, Jun 5, 2013 at 3:06 PM, tarak karmakar <tarak20...@gmail.com> wrote:
> One more query Justin. > Even if I don't use any sort of constraints in the final run, I'm not > getting the initial temperature as exactly 300 K. Initial part of the .log > file is as follows > > > Initial temperature: 297.694 K > > Started mdrun on node 0 Wed Jun 5 16:58:40 2013 > > Step Time Lambda > 0 0.00000 0.00000 > > Energies (kJ/mol) > Bond U-B Proper Dih. Improper Dih. CMAP Dih. > 8.53037e+03 1.41675e+04 8.92031e+03 8.51469e+02 -2.03250e+03 > LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) > 4.38857e+03 7.54455e+04 3.60795e+05 -8.59592e+03 -2.71243e+06 > Coul. recip. Potential Kinetic En. Total Energy Temperature > -2.16435e+05 -2.46639e+06 4.69142e+05 -1.99725e+06 2.97697e+02 > Pres. DC (bar) Pressure (bar) > 0.00000e+00 2.49064e+02 > > > Is it the normal case in gromacs? Or, it is because of my system? > I see in lammps, generating the initial temp shows the exact number as > specified in the input file at zeroth step. (not my system but a small test > system) > GROMACS is doing what was asked of it - see manual 7.3.17. The distribution of values sampled from a given distribution generally will not have an average that equals that given distribution. Whatever LAMMPS does is its own business :-) Mark On Wed, Jun 5, 2013 at 1:57 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 6/4/13 12:51 PM, tarak karmakar wrote: > > > >> 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? > >> > >> > > You can generate velocities whenever you like, but you'll have to allow > > for some time to equilibrate, so what you're calling "production" isn't > > entirely production because it's no longer equilibrated in any real > sense. > > The heating phase may help to optimize the initial geometry, but > > regenerating velocities may screw everything up if something becomes > > unstable. Assuming restraints are off during "production," then you can > > screw up the geometry of your system if something gets an unpleasant kick > > from the new velocities. > > > > -Justin > > > > 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://vt.edu/Pages/Personal/justin> > >>> <h**ttp://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> > >>> <htt**p://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<h**ttp://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> > >>> <http://**www.gromacs.org/Support/**Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > >>> > > >>> > >>> > > -- > > ==============================**========== > > > > 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 > -- 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
