Re: membrane system

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Sep 21 2011 - 02:44:42 CDT

Hi Ipsita,

What thermodynamic ensemble do you run the simulation in?

Jerome

On 21 September 2011 08:30, ipsita basu <ibasu788_at_gmail.com> wrote:
> Sorry to disturb you again but I sent you mails before regarding this
> problem but didn't get any reply from your end.
> I have a membrane monolayer system, to make stable this monolayer I
> use vaccuam, and to do this I twice the length of the simulation box
> in z direction(membrane normal axis> in cellbasis vector option. But
> after 8 to 10 ns the waters are again jumping to the lipid end. Will
> you please tell me how to fix this?
> Another question is if I use 2D option in cellbasis vector, the can
> avoid the water jumping problem, but using 2D it will not be possible
> to use PME. Is it okay to run without using PME?
> Any kind of help from your end is really needed.
> Thanking you,
> Ipsita
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
>
>

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