Thanks for the information Flo. Before doing NPT I have already equilibrated my system by heating it from 0K to 300K in 300 ps, then the pressure has reached to 1 bar. Now while doing NPT I'm getting the excess pressure. Is there any problem with the coupling constant ? I am checking it by taking different tau_p values. Let's see.
On Wed, Nov 21, 2012 at 1:16 AM, Florian Dommert <domm...@icp.uni-stuttgart.de> wrote: >> -----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 -- Tarak -- 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
