[gmx-users] Reg: NPT Equilibration of water
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Oct 29 10:36:49 CEST 2010
On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote:
> I am using the semiisotropic pressure scaling because i want the box
> size to remain the same as that of the original box size in X and Y
> axis and want to change it only on the Z axis. I am doing this because
> at a latter stage i want to create an interface with organic solvent
> where i need the cross sections (X and Y axis length) of both the box
> should be the same.
>
> what i should do now get the pressure of 1 bar?
7 +/- 500 *is* approximately 1 bar, and hardly any better an
approximation than 1 +/- 500. If you want lower fluctuations, use a
larger system and run for a much longer time. Or, since you'll have to
re-equilibrate once you combine the solvent boxes, don't bother.
Mark
>
> Has no one has got the pressure of water to be close to 1 bar in
> GROMACS till now?
>
> Regards
> Vinoth
>
> On Fri, Oct 29, 2010 at 12:54 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> 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>
> <mailto: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
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
>
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> 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 <mailto:spoel at xray.bmc.uu.se>
> http://folding.bmc.uu.se
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101029/4137052f/attachment.html>
More information about the gromacs.org_gmx-users
mailing list