Re: membrane system

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Sep 21 2011 - 03:47:16 CDT

What do you expect to happen if there is a empty region in the
simulation box and you run NPT?

Jerome

On 21 September 2011 10:15, ipsita basu <ibasu788_at_gmail.com> wrote:
> I am using NPT ensemble.
>
> On 9/21/11, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>> 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
>>>
>>>
>>
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:24 CST