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


From: Xikai Jiang
Subject: Re: [ESPResSo-users] Question about simulation of water
Date: Mon, 6 Oct 2014 00:16:59 -0400

Dear Marcello:

Thank you for your help and scripts. I can run your script and the pressure is steady.

My script for NVT SPC/E water can run with steady pressure with a value of about -14000 bar. Then I continued from the last configuration from NVT and run NPT simulation, the box size becomes steady at 2.77nm in each direction, the box size should be around 3.1nm for 1000 water molecules at 1 bar. Is this related to the rigid bond pressure?

I have attached my code for NPT simulation.

Regards,

Xikai

> Date: Sun, 5 Oct 2014 22:55:26 +0200
> Subject: Re: [ESPResSo-users] Question about simulation of water
> From: address@hidden
> To: address@hidden
> CC: address@hidden
>
> Hi,
>
> > 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.
>
> Cheers,
>
> Marcello
>
>
>
> 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 http://goo.gl/zlIZix

Attachment: confout
Description: Binary data

Attachment: functions.tcl
Description: Tcl script

Attachment: npt_spce.tcl
Description: Tcl script


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