[gmx-users] Dubious results with NPT
sujithkakkat .
sujithks58 at gmail.com
Fri Mar 14 15:02:40 CET 2014
Hello Mark,
I guess you were asking whether I ran the simulation as a
continuation to a previous 5ns run?
But the results I got are from a continuous 10ns simulation.
Sujith.
On Fri, Mar 14, 2014 at 4:28 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> 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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