[gmx-users] lipid membrane study and the increase in z dimension on dppc128.gro

[rama david]

Dear Justin,

         I added the water as per your instruction and following the
instruction from
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
 I change the box size by editconf and  vdwradii.dat  files carbon radii to
0.45.
I added the water with the genbox command.
       I found that most water molecule are up to the N4, some are up to
the Phosphate
and few may be up to the 013, and 016. but no one is bellow this.

Is this behaviour is right ???  or should I need also the script
keepbyz.py to run on the system??


I not get the any warning while Energy minimization,  NVT, NPT and MD  (
that
 mean system was not unstable and blown away)



I am looking forward for suggestions


With best regards,
RamaDavid.





On Fri, Oct 10, 2014 at 5:26 PM, rama david <ramadavidgroup at gmail.com>
wrote:

> Dear Justin,
>           Thank you.
>
>
> With regards,
> Rama david
>
> On Fri, Oct 10, 2014 at 5:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/10/14 7:51 AM, rama david wrote:
>>
>>> Dear Justin,
>>>   Thank you  a lot for immediate reply.
>>>   One more question:
>>>     Should I need to equilibriate the membrane after this one  ??
>>>
>>>
>> Even Tieleman's pre-equilibrated membranes are only from a few ns of
>> simulation time; I would always equilibrate much longer.  So of course in
>> the case where you change the system even more, you should definitely
>> equilibrate.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>