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Re: [ESPResSo-users] Question about simulation of water

From: Marcello Sega
Subject: Re: [ESPResSo-users] Question about simulation of water
Date: Sun, 5 Oct 2014 22:55:26 +0200


> rigid bonds is not included. I'm thinking will this cause the problem?

in principle it should just give you an offset to the pressure, but it
should not make it diverge.

I couldn't test you script because functions.tcl is missing, but I
found an old script for SPC water, which I wrote some time ago: it
still works fine with espresso 3.2 (in attachment).

Please check it out. If the pressure diverges also using this script,
send me details about the version of espresso you're using, plus your
config file, and I will try to investigate.



On Sun, Oct 5, 2014 at 9:07 PM, Xikai Jiang <address@hidden> wrote:
> The SPC/E model treats water as a rigid molecule, and the O-H and H-H bonds
> are all rigid simulated by Rattle-Shake algorithm. According to the manual,
> section 8.1.22. Pressure, it mentions that the pressure contribution for
> rigid bonds is not included. I'm thinking will this cause the problem?
> Best,
> Xikai
>> Date: Tue, 30 Sep 2014 21:45:15 +0200
>> From: address@hidden
>> To: address@hidden; address@hidden
>> Subject: Re: [ESPResSo-users] Question about simulation of water
>> Dear Fei,
>> this is a well-known problem for solvent box equilibration.
>> Increase the initial distance between the water molecules and start with
>> a NVT simulation.
>> NVT allows you to find a somehow equilibrated structure with a wrong
>> density.
>> After that and under consideration of the final NVT snapshot, you can
>> probably perform some NPT without exploding pressure to achieve the
>> correct density.
>> Best regards,
>> Jens
>> On 09/29/2014 10:10 PM, Fei Zhang wrote:
>> > Dear All,
>> >
>> > I am doing a simulation of pure water using Espresso now. However,
>> > when I did the NVT simulation, the pressure always blow up. I used
>> > SPC/E water model and used rigid bond for the bond between O and H.
>> > Can anyone help me with this problem?
>> >
>> > The script is attached.
>> >
>> > Thank you.
>> >
>> > Fei
>> --
>> ================
>> Dr. Jens Smiatek
>> Institute for Computational Physics
>> University of Stuttgart
>> Allmandring 3
>> 70569 Stuttgart
>> Germany
>> Office: 1.032
>> Phone: +49-(0)711/685 63757
>> E-Mail: address@hidden

Institut f├╝r Computergest├╝tzte Biologische Chemie
University of Vienna
PGP public key on MIT server

Attachment: pure_water.tcl
Description: Tcl script

Attachment: spc216.gro
Description: Binary data

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