[gmx-users] Dubious results with NPT
Mark Abraham
mark.j.abraham at gmail.com
Fri Mar 14 11:58:50 CET 2014
The simplest explanation would be that you've appended to a previous 5ns
trajectory, not run a new trajectory. Check the .log file and the length of
time you expected this job to run (wall and simulation).
Mark
On Fri, Mar 14, 2014 at 9:02 AM, sujithkakkat . <sujithks58 at gmail.com>wrote:
> Hello,
>
> This time I tried sesiisotropic scaling with Berendsen Barostat. The
> compressibility was set to zero in Z-direction allowing scaling only in X
> and Y. The NPT simulation was run for 10ns.
> The result did not look good and the average pressure was ~36 bar
> (reference pressure is 1 bar).
> Even more confusing was the graphs of various properties against time.
> Pressure vs time shows a sudden decrease in fluctuations at about 5ns and
> thereafter . The pressure fluctuations lowered to around ~170bar from ~650
> bar.
> A dramatic change was observed in many properties at around this time. For
> eg, the short range LJ interaction was found to decrease sharply at ~5ns.
> Also, total energy, Kinetic, Potential energies and the temperature showed
> a rapid drop in the magnitude of their fluctuations from the same time.
>
> Nothing notable was observed in the system trajectory at around this
> time. I am totally confused, and I feel that I made some very bad choice
> again the MDP file given below.
> Please let me know what you think. Suggest something on this issue which I
> should read about.
>
>
> ; 7.3.3 Run Control
> integrator = md
> tinit = 0
> dt = 0.001
> nsteps = 10000000
> comm_mode = Linear
> nstcomm = 1
> comm_grps = CHX SOL
>
> ; 7.3.8 Output Control
> nstxout = 25000
> nstvout = 25000
> nstfout = 25000
> nstlog = 100
> nstenergy = 100
> nstxtcout = 100
> xtc_precision = 1000
> xtc_grps = System
> energygrps = System
>
> ; 7.3.9 Neighbor Searching
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 0.9
>
> ; 7.3.10 Electrostatics
> coulombtype = PME
> rcoulomb = 0.9
>
> ; 7.3.11 VdW
> vdwtype = cut-off
> rvdw = 1.4
> DispCorr = EnerPres
>
> ; 7.3.13 Ewald
> fourierspacing = 0.12
> pme_order = 4
> ewald_rtol = 1e-5
>
> ; 7.3.14 Temperature Coupling
> tcoupl = nose-hoover
> tc_grps = CHX SOL
> tau_t = 0.5 0.5
> ref_t = 298 298
>
> ; 7.3.15 Pressure Coupling
> pcoupl = berendsen
> pcoupltype = semiisotropic
> tau_p = 2.0
>
> compressibility = 4.5e-5 0.0
> ref_p = 1.0 1.0
>
>
> ; 7.3.17 Velocity Generation
> gen_vel = no
> gen_temp = 298
> gen_seed = -1
>
> ; 7.3.18 Bonds
> constraints = none
> constraint_algorithm = LINCS
> continuation = no
> lincs_order = 4
> lincs_iter = 1
> lincs_warnangle = 30
>
>
>
> Regards,
> Sujith.
>
>
> On Wed, Mar 12, 2014 at 5:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 3/12/14, 7:51 AM, sujithkakkat . wrote:
> >
> >> Hello,
> >>
> >> After a while I got back to the problem posted here. This issue was
> the
> >> large value for average pressure(~25 bar against the reference pressure
> >> of
> >> 1 bar) in NPT simulations with parrinello rahman barostat. The system
> >> studied is cyclohexane-water system with an interface.
> >> The forcefield is Gromos96. Gromacs 4.6.5 version is used.
> >>
> >> I recollect a post from Michael Shirts which says that with systems that
> >> are heterogeneous in direction (not uniform in x y and z), any errors in
> >> the pressure may be magnified. Is this what is happening in my case?
> >>
> >> Based on your suggestions , I tried the following to analyze/solve the
> >> problem, and till now the results have not improved a bit.
> >>
> >> (i) The system was simplified. Each phases was simulated separately.
> The
> >> results were good, with proper values of average pressure after NPT
> >> simulation for both independent water and cyclohexane systems. However,
> >> when doing the same with similar parameters on the water-cyclohexane
> >> combined system with parrinello-rahman barostat , still gives very high
> >> average pressure (even after 10ns )
> >>
> >> (ii) Changing the tau_p values did not help either. (I tried 1ps, 2ps,
> >> and 4ps)
> >>
> >> My question is whether, I can try the semiisotropic scaling? The manual
> >> says that it is useful in case of systems with interface. I am not
> sure,
> >> since none of the replies I got suggested that option, which gives the
> >> impression that it is not the best solution. But , to my limited
> knowledge
> >> that is the only option left to be tried to solve the issue.
> >>
> >>
> > Worth a shot. Also try changing the barostat to Berendsen to see if that
> > changes anything. There are a lot of interrelated issues here, possibly
> a
> > problem with the barostat, the tau_p value, the type of coupling, the
> > combination of the integrator and barostat...you see how complicated it
> > gets, and that's only some of the possible issues.
> >
> > -Justin
> >
> >
> >
> >> The mdp file used is,
> >>
> >> ; 7.3.3 Run Control
> >> integrator = md
> >> tinit = 0
> >> dt = 0.001
> >> nsteps = 10000000
> >> comm_mode = Linear
> >> nstcomm = 1
> >> comm_grps = CHX SOL
> >>
> >> ; 7.3.8 Output Control
> >> nstxout = 25000
> >> nstvout = 25000
> >> nstfout = 25000
> >> nstlog = 100
> >> nstenergy = 100
> >> nstxtcout = 100
> >> xtc_precision = 1000
> >> xtc_grps = System
> >> energygrps = System
> >>
> >> ; 7.3.9 Neighbor Searching
> >> nstlist = 10
> >> ns_type = grid
> >> pbc = xyz
> >> rlist = 0.9
> >>
> >> ; 7.3.10 Electrostatics
> >> coulombtype = PME
> >> rcoulomb = 0.9
> >>
> >> ; 7.3.11 VdW
> >> vdwtype = cut-off
> >> rvdw = 1.4
> >> DispCorr = EnerPres
> >>
> >> ; 7.3.13 Ewald
> >> fourierspacing = 0.12
> >> pme_order = 4
> >> ewald_rtol = 1e-5
> >>
> >> ; 7.3.14 Temperature Coupling
> >> tcoupl = nose-hoover
> >> tc_grps = CHX SOL
> >> tau_t = 0.5 0.5
> >> ref_t = 298 298
> >>
> >> ; 7.3.15 Pressure Coupling
> >> pcoupl = parrinello-rahman
> >> pcoupltype = isotropic
> >> tau_p = 2.0
> >> compressibility = 4.5e-5
> >> ref_p = 1.0
> >>
> >>
> >> ; 7.3.17 Velocity Generation
> >> gen_vel = no
> >> gen_temp = 298
> >> gen_seed = -1
> >>
> >> ; 7.3.18 Bonds
> >> constraints = none
> >> constraint_algorithm = LINCS
> >> continuation = no
> >> lincs_order = 4
> >> lincs_iter = 1
> >> lincs_warnangle = 30
> >>
> >>
> >>
> >> Please comment.
> >>
> >> Sujith.
> >>
> >>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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