Reply inline... On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul <[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 > > 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 > 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 | (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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