> -----Ursprüngliche Nachricht----- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Justin Lemkul > Gesendet: Dienstag, 20. November 2012 18:33 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] pressure_coupling > > > > On 11/20/12 12:29 PM, tarak karmakar wrote: > > 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 ? > > > > I have no personal experience with the md-vv/MTTK combination. The way to > test if there is a bug or something is to take an equilibrated system (as suggested > before) and continue it with the desired parameters. If they deviate or > incorrectly report pressure, then there's probably a bug. I'm not ready to > conclude that until it is tested though. > > -Justin >
I once tried to use the same combination of T and P coupling and MD-vv for a system, which could be simulated with PR at 1bar without problems. But I also observed this large pressure. Somehow I have in mind, that there was recently a thread about MTTK coupling on the list with the conclusion that MTTK is so far not stable, but please check the archives to assure this. /Flo > > 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 > > > > > > > > - > > > > -- > ======================================== > > 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? Read http://www.gromacs.org/Support/Mailing_Lists
