Hi, all- There are some issues with MTTK + constraints that are being worked out for 4.6. The good thing is, I have developed some sensitive tests of the correct volume distribution (see http://arxiv.org/abs/1208.0910) and the errors in PR are very, very small. I would recommend using md + PR for projects with code before 4.6.
On Thu, Nov 22, 2012 at 4:27 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 tarak karmakar >> Gesendet: Donnerstag, 22. November 2012 10:15 >> An: Discussion list for GROMACS users >> Betreff: Re: [gmx-users] pressure_coupling >> >> 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 > > Yes, that is right. The reason might be, that it is stable, working with > Leap-Frog and implemented in Gromacs. However actually PR does not produce > an NpT but an isoenthalpic ensemble. It also does not conform to both > pressure virial theorems (see appendix of the Nose paper cited in the > Gromacs manual). For this reason it would be very very good, if MTTK would > work in Gromacs, because it fulfills all requirements for an NpT ensemble. > On the other hand side the deviations vanish in the thermodynamic limit, so > if your system is large enough, there should be no significant difference. > > /Flo > >> >> 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? 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 > > -- > 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