It's in review with JCTC right now.
On Thu, Nov 22, 2012 at 2:19 PM, ABEL Stephane 175950 <stephane.a...@cea.fr> wrote: > Hello, > > This is a very nice and interesting work, Michael. Thank you for the efforts > you made in writing this paper. I hope you will publish it. > > Best > > Stephane > > > ________________________________________ > > 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: >>> -----Urspr?ngliche 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 f?r Computerphysik >>> > Universit?t Stuttgart >>> > Allmandring 3 >>> > D-70569 Stuttgart >>> > >>> > Tel.: 0711-68563613 >>> > Fax: 0711-68563658 >>> > >>> > >>> >> -----Urspr?ngliche 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: >>> >> >> -----Urspr?ngliche 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? 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