Thanks Justin for the quick reply. Is there any problem with the algorithms ??
I have used Velocity Verlet , Nose-Hoover and MTTK combination. SHAKE has been used to constrains the H-covalent bonds. tau_t = 1 ps tau_P = 1 ps I got the mean pressure at ~130 bar. Previously with the same initial coordinates I have used Leap-Frog, NH, Parinello-Rehman with LINCS to constrain H-covalent bonds. tau_t was 0.1 ps and tau P was 2 ps. The I have seen the pressure fluctuating around 1 bar( as expected) So can you please inform me from where this problem is coming - algorithms and/ tau_t and tau_P parameters ? On Tue, Nov 20, 2012 at 10:10 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/20/12 11:26 AM, tarak karmakar wrote: >> >> Dear All, >> >> I want to keep the pressure at 1.0 bar during the NPT simulation. But >> it is fluctuating around 130 bar. So can anyone please inform me >> whether I have missed any keyword in my .mdp file OR is it because of >> the tau_p which I set 1s 1.0 ps. > > > Equilibrate with a weak coupling method (Berendsen) and then proceed using > better algorithms. > > -Justin > > >> Thanks >> >> The .mdp file is given below >> >> >> >> ; 7.3.3 Run Control >> integrator = md-vv ; md integrator >> tinit = 0 ; [ps] starting time for >> run >> dt = 0.001 ; [ps] time step for >> integration >> nsteps = 15000000 ; maximum number of >> steps to integrate, 0.001 * 15,00,000 = 15 ns >> nstcomm = 1 ; [steps] frequency of >> mass motion removal >> comm_grps = Protein Non-Protein ; group(s) for center >> of mass motion removal >> >> ; 7.3.8 Output Control >> nstxout = 10000 ; [steps] freq to write >> coordinates to trajectory >> nstvout = 10000 ; [steps] freq to write >> velocities to trajectory >> nstfout = 10000 ; [steps] freq to write forces >> to trajectory >> nstlog = 1000 ; [steps] freq to write >> energies to log file >> nstenergy = 1000 ; [steps] freq to write >> energies to energy file >> nstxtcout = 1000 ; [steps] freq to write >> coordinates to xtc trajectory >> xtc_precision = 1000 ; [real] precision to write >> xtc trajectory >> xtc_grps = System ; group(s) to write to xtc >> trajectory >> energygrps = System ; group(s) to write to energy file >> >> ; 7.3.9 Neighbor Searching >> nstlist = 1 ; [steps] freq to update neighbor >> list >> ns_type = grid ; method of updating neighbor list >> pbc = xyz ; periodic boundary conditions >> in all directions >> rlist = 1.2 ; [nm] cut-off distance for >> the short-range neighbor list >> >> nsttcouple = 1 >> nstpcouple = 1 >> >> ; 7.3.10 Electrostatics >> coulombtype = PME ; Particle-Mesh Ewald >> electrostatics >> rcoulomb = 1.2 ; [nm] distance for Coulomb >> cut-off >> >> ; 7.3.11 VdW >> vdwtype = cut-off ; twin-range cut-off with >> rlist where rvdw >= rlist >> rvdw = 1.2 ; [nm] distance for LJ cut-off >> DispCorr = EnerPres ; apply long range dispersion >> corrections for energy >> >> ; 7.3.13 Ewald >> fourierspacing = 0.12 ; [nm] grid spacing for FFT >> grid when using PME >> pme_order = 4 ; interpolation order for PME, 4 = >> cubic >> ewald_rtol = 1e-5 ; relative strength of >> Ewald-shifted potential at rcoulomb >> >> ; 7.3.14 Temperature Coupling >> tcoupl = Nose-Hoover ; Nose-Hoover >> temperature coupling >> tc_grps = Protein Non-Protein ; groups to >> couple seperately to temperature bath >> tau_t = 1.0 1.0 ; [ps] time >> constant for coupling >> ref_t = 300 300 ; [K] >> reference temperature for coupling >> >> ; 7.3.15 Pressure Coupling >> pcoupl = MTTK ; pressure coupling >> where box vectors are variable >> pcoupltype = isotropic ; pressure coupling in >> x-y-z directions >> tau_p = 1.0 ; [ps] time constant >> for coupling >> compressibility = 4.5e-5 ; [bar^-1] compressibility >> ref_p = 1.0 ; [bar] reference >> pressure for coupling >> >> ; 7.3.17 Velocity Generation >> gen_vel = no ; velocity generation turned off >> >> ; 7.3.18 Bonds >> constraints = h-bonds >> constraint_algorithm = SHAKE ; SHAKE Constraint Solver >> shake_tol = 1.0e-5 >> >> > > -- > ======================================== > > 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 > > ======================================== > -- > 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? 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