[gmx-users] Dubious results with NPT

[Justin Lemkul]

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

==================================================