From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Oct 23 2013 - 07:30:36 CDT
Please search the NAMD maling list archives before posting. This topic has
been discussed before<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/15454.html>.
In short the membrane is drifting a bit, but that is nothing to worry
about, after all you are using periodic boundary conditions. You can always
postprocess the directory to keep the membrane center of mass at z=0.
Btw, Do you have zeroMomentum yes in your conf file?
Regards,
Ajasja
On 23 October 2013 12:46, Villalain Boullon, Jose <jvillalain_at_umh.es> wrote:
> Dear All,****
>
> ** **
>
> First of all, thank you very much for your help. It is always encouraging
> that you can rely on people pertaining to this forum to resolve the
> problems which arise trying to work with NAMD (at least for me as a newbie).
> ****
>
> ** **
>
> Sorry, but I have a new problem which I have not seen previously. I am
> using the configuration files from the membrane-protein tutorial, but some
> simulations, not all, show that there is a displacement of the water
> layer/membrane structure. I will try to explain. The water thickness of one
> layer increases steadily as the other one decreases steadily, like water is
> moving from one layer to the other. Seen from the other way, it is like the
> whole membrane is moving, downwards/upwards.****
>
> ** **
>
> Any hint to resolve this strange behaviour ?****
>
> Best regards,****
>
> Jos.****
>
> ** **
>
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