Reply inline... On Thu, Jul 15, 2010 at 9:54 AM, Justin A. Lemkul <[email protected]> wrote:
> > > Sai Pooja wrote: > >> Reply inline... >> >> >> On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Sai Pooja wrote: >> >> Hi, >> >> I have a system of 3600 LJ particles in a plane (using >> freeze-dimension option in z). I am running npt runs using >> Semi-isotropic pressure coupling with Parrinello-Rahman >> barostat. I have a few concerns: >> >> 1) On the gromacs website, a webpage mentions that this type of >> pressure coupling may not be accurate >> >> >> Please provide a link when making this kind of statement. >> >> http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman >> < >> http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman >> > >> > > Bugzilla entry 14 is ancient, and has long since been resolved: > > > http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0#Resolved_issues > > > >> 2) It takes a really long time for the system to reach the >> reference pressure > 500ns. Particularly the Pxx, Pyy terms are >> very different and take an extremely long time to converge to a >> common value. >> >> integrator = md >> dt = 0.001 >> nsteps = 50000000 >> >> ; OUTPUT CONTROL OPTIONS >> nstxout = 0 ; No output, except for last frame >> (coordinates) >> nstvout = 0 ; No output, except for last frame >> (velocities) >> nstfout = 0 ; No output, except for last frame >> (forces) >> nstlog = 1000000 ; Write every nth step to the log >> nstenergy = 1000000 ; Write energies at every n step >> nstxtcout = 1000000 ; Do not write a compressed tr >> >> ; NEIGHBORSEARCHING PARAMETERS >> nstlist = 10 >> ns-type = Grid >> pbc = xyz >> rlist = 0.9 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> coulombtype = Cut-off >> rcoulomb = 1.1225 >> vdw-type = User >> rvdw = 1.1225 >> table-extension = 0 >> >> ; Temperature coupling >> tcoupl = nose-hoover >> tc-grps = ARAR >> tau_t = 0.1 >> ref_t = 120.2717 >> >> ; Pressure coupling >> pcoupl = Parrinello-Rahman >> pcoupltype = semiisotropic >> tau-p = 1.0 1.0 >> compressibility = 1e-5 0 ;Dont know >> ref-p = 69 0 >> >> >> ;Generate velocities for startup run >> gen_vel =no >> gen_temp =120.2717 >> gen_seed =-1 >> >> ;Non equilibrium MD steps >> freezegrps =ARAR >> freezedim =N N Y >> ;Constraints >> constraints = all-bonds >> constraint_algorithm = Lincs >> lincs_order = 4 >> lincs_iter = 1 >> lincs_warnangle = 90 ;unconstrained_start = no >> ;shake_tol = 0.0001 >> >> > Do you run any equilibration prior to applying these parameters? Both N-H > and P-R allow for wide fluctuations in temperature and pressure, > respectively, which are exacerbated by systems that are not sufficiently > equilibrated. Hence it could take a very long time if you do not > equilibrate well using, i.e. a weak coupling scheme first. > > I usually start with a pressure nearby. For example, I start with a system which was equilibrated at p=71 and then run npt at p=69. Is that not sufficient? Pooja > -Justin > > >> >> >> What was your equilibration protocol? What are your .mdp settings? >> >> -Justin >> >> >> Pooja >> >> -- Quaerendo Invenietis-Seek and you shall discover. >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> 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 [email protected] >> <mailto:[email protected]> >> >> http://lists.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 [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Quaerendo Invenietis-Seek and you shall discover.
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