U r right FLorian I have also tried playing around the tau_p but in vain. Even in absence of any constraints, it is giving almost same result. Em thinking to move again to Leap-Frog, NH , PR. I see people generally use this combination a lot. Thanks
Tarak On Wed, Nov 21, 2012 at 8:08 PM, Florian Dommert <domm...@icp.uni-stuttgart.de> wrote: > > > ------- > Florian Dommert > Dipl. Phys. > > Institut für Computerphysik > Universität Stuttgart > Allmandring 3 > D-70569 Stuttgart > > Tel.: 0711-68563613 > Fax: 0711-68563658 > > >> -----Ursprüngliche Nachricht----- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von tarak karmakar >> Gesendet: Mittwoch, 21. November 2012 15:03 >> An: Discussion list for GROMACS users >> Betreff: Re: [gmx-users] pressure_coupling >> >> 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. >> > > I don't think that playing around with the coupling constant will help you. > You can set it to extreme values, but you won't see any difference. The > coupling constant determines, how fast the system pressure should relax to > the reference pressure. I would see a better possibility to play around by > simulating for a longer time. Then observing the variation of the pressure > in time, the size of the fluctuation and the excess pressure. Perhaps > something will change, but I don't think so. I play around with the coupling > constants but observed no change. > > Maybe, but this is really speculation, there is a problem with the > combination of constraints and MTTK. Please check the archives of the user > and developer list to obtain more information. > > /Flo > >> >> 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 > > -- > 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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