[gmx-users] Re: gmx-users Digest, Vol 66, Issue 85

[Pan Wu]

Thanks Dr. Dallas Warren. I have plotted the picture of pressure with
respect to simulation time, it is not fluctuation, it
is monotonically decrease from about 500 to 3 bar, this is why I am
confused.

If it really should take some time to converge the required pressure, my MD
simulation is 4 ns, during the whole simulation time, the pressure keeps on
decrease. (Will this pressure convergence take that long time?)

The initial box size is 12 ns *12 ns *12 ns, after the simulation, it turned
out to be 52 * 52 *52 .


> ---------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 12 Oct 2009 14:32:19 +1100
> From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
> Subject: RE: [gmx-users] Pressure problem: pressure is too large
>        during  MDsimulation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <89907EA1DCFB7548A431C13A270F9DD50859202D at prk-exch-01.vcp.local>
> Content-Type: text/plain; charset="us-ascii"
>
> Plot the fluctuations of the pressure with time for the simulation.  Far
> better way I think to get an idea of what is going on with a property
> than just looking at values in a log file.  Especially when you are
> starting out.
>
>
>
> With pressure coupling, it is not unusual to have a fluctuation of a
> hundred or so.  And that is nothing to worry about, entirely normal
> behaviour to observe.  And with such large fluctuations, the average
> pressure can deviate from the reference pressure.  Of course, with more
> sample points and longer simulation time, it will get closer to the
> reference value.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
> Department of Pharmaceutical Biology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
>
>
>
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Pan Wu
> Sent: Monday, 12 October 2009 2:20 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Pressure problem: pressure is too large during
> MDsimulation
>
>
>
> Hi gmx users,
>
>    I am now simulating one protein with solvent, in all atom
> forcefield, gromacs official distributed version. The pressure of system
> seems to be unreasonable large, and during the whole process, the box
> keeps increasing.
>
>    Here is how I set up the system,
>
>    1. I solvate the proteini use spc216.gro, the log file shows:
>
>                 Output configuration contains 40990 atoms in 12386
> residues
>
>                 Volume: 412.593 (nm ^3)
>
>                 Density: 1015.79 g/L
>                 Number of SOL molecules: 13410
>
>
>
>     2. Then I start to do MD with constrains (40 ps), then MD without
> constrains.
>
>                The md.log shows pressure keeps decrease, start from
> 5.79 e+02  until at last to about 3.14e+00, so you can see how large the
> box size is enlarged.
>
>         However in my setup, what I use for P-coupling is the same:
>
>               Pcoupl = Berendsen
>
>               Pcoupltype = isotropic
>
>               tau_p = 0.5
>
>               compressibility = 4.5e-5
>
>               ref_p = 1.0
>
>
>
>          my integral step size is 1fs, so the tau_p = 0.5 ps should be
> enough. Also I checked the temperature, it is constant during the MD
> process. (303K)
>
>
>
>         So from these setup process, I think: the density is correct
> for solvent water and system; the compressibility is chosen as for
> standard water, the ref_p is chosen as 1.0. Why the pressure is so
> large?
>
>
>
>      Thank you in advance!
> --
> Sincerely
> =================================
> Pan Wu
> Graduate Student in Department of Chemistry
> Duke University
> 124 Science Drive
> 5301 French Family Science Center
> Durham, NC 27708
> Phone: (919) 660-1583
> =================================
>
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> End of gmx-users Digest, Vol 66, Issue 85
> *****************************************
>



-- 
Sincerely
=================================
Pan Wu
Graduate Student in Department of Chemistry
Duke University
124 Science Drive
5301 French Family Science Center
Durham, NC 27708
Phone: (919) 660-1583
=================================
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