[gmx-users] Reg: NPT Equilibration of water

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 29 09:24:13 CEST 2010

```On 2010-10-29 09.08, vinothkumar mohanakrishnan wrote:
>
> Hi Mark
>
> I read the link before posting the question. even though the fluctation
> is between 500-600 (as said in the link) bar the average pressure is
> around 7.4 bar. my concern is the average pressure?. Because at a latter
> stage i am going to combine this water box with another organic solvent
> and i want to avoid any complications there.

Think again of what you just wrote. Your value is 7 +/- 500. In fact
according to normal statistical rules you should round the value of 7 to
0. If you want more accurate number you could increase the box size by a
factor of 100.

By the way, why are you using semiisotropic pressure scaling in a water box?

>
> Regards
> Vinoth
>
> On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote:
>
>         Hi Gromacians
>
>         I want to do equilibration of water (spc model) first in the NVT
>         ensemble and then in the NPT ensemble to maintain a temperature
>         of 300K and a pressure of 1 bar respectively. The NVT
>         equilibration works fine and the average temperature turns out
>         to be 299.229 K.
>
>         Energy                      Average       RMSD        Fluct.
>               Drift            Tot-Drift
>         ------------------------------
>         -------------------------------------------------
>         Temperature                 299.229    10.3092    10.2463
>           0.0393873    3.93877
>         Heat Capacity Cv:       12.494 J/mol K (factor = 0.00118698)
>
>           when i do NPT equilibration i am not getting the desired
>         pressure as 1 bar or atleast close to 1 bar (between 1-1.4 bar).
>         In the mdp file i used semiisotropic pressure coupling type
>         because i want to fix the length of the box same on two axis as
>         that of the original box size and want to change it only on one
>         axis. can any one tell me why iam not getting the desired
>         pressure of 1 bar?.
>
>
>     This looks normal for a smallish water system over 100ps. See
>     http://www.gromacs.org/Documentation/Terminology/Pressure
>
>     Mark
>
>
>
>         Energy                      Average       RMSD     Fluct.
>           Drift  Tot-Drift
>         -------------------------------------------------------------------------------
>         Pressure (bar)               7.4339    574.052    573.574
>         0.812129    81.2138
>
>         Given below is my mdp file (NPT equilibration). any help is
>         highly appreciated.
>
>         title           = DCE NVT equilibration
>         cpp           = usr/bin/cpp
>         integrator   = md
>         nsteps       = 100000
>         dt              = 0.001
>         nstxout       = 100
>         nstvout       = 100
>         nstenergy   = 100
>         nstlog        = 100
>         ns_type     = grid
>         nstlist        = 1
>         rlist            = 1.0
>         coulombtype    = PME
>         rcoulomb         = 1.0
>         vdwtype          = Cut-off
>         rvdw               = 1.0
>         pme_order       = 4
>         fourierspacing  = 0.16
>         pbc                 = xyz
>         tcoupl              = V-rescale
>         tc-grps             = system
>         tau_t                = 0.1
>         ref_t                 = 300
>         pcoupl              = berendsen
>         pcoupltype        = semiisotropic
>         tau_p                = 0.5
>         ref_p                 = 1.0 1.0
>         compressibility   = 0.0 4.5e-5
>         DispCorr            = Enerpres
>         gen_vel             = yes
>         gen_temp          = 300
>         gen_seed          = 173529
>
>         Regards
>         Vinoth
>
>
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>

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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