[gmx-users] Re:Unequal water of Bilayer system in *PR step

[Xavier Periole]

On Fri, 26 Sep 2008 07:30:13 -0400
  "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 
> 
> sudheer babu wrote:
>> -
>> 
>> 
>>      
>>      > Hi Users,
>>      >     I have extended the lipid bilayer(popc) from default
>>     popc128a.pdb to
>>      > 200 popc molecules with suffcient water by using genbox.
>>      > genbox -cs  128a.pdb -o  out.gro  -p  128a.top -box 9.2 9.2 6.9,
>>      to the
>>      > out.gro(contain 200 popc) minimisation ran fine later swtich over
>>     to *PR
>>      > with fc-1000 on P8,C51,C53 of popc and saw output_pr.gro in VMD
>>      water has
>>      > weird strcuture(up side downs but popc structure is quite fine).
>>      > So I have reduced the pbc box size to 9 9 6.7  with *editconf
>>     later I ran
>>      > minimsation and *PR, "now water" and POPC structures are "fine" but I
>>      > observed "unequal water".
>> 
>>  
>> 
>>     What do you mean with "unequal water"?
>> 
>>         Thanks for the response unequal water means ' when I noticed the 
>> intial 200popc.gro use VMD water molecules present bothsides almost same 
>> towards corners of the simulation box and centre of the above and below 
>> popc heads but after *PR one side of the leaflet bilayer corners have 
>> very less water (say 20 water molecules earlier 80 water molecules) 
>> looks at corners doesnt have water seems. I hope you understood my problem,
>> 
> 
> Probably your system isn't perfectly centered within the box and you are 
>seeing "diffusion" from PBC.
It is however not totally clear (to me) what is the problem. If it is a
change of water density in a particular area of the simulation box, it could
well be that the water distribution was not so "ideal" in your starting
configuration.
Justin suggestion "run a bit longer" is good. especially that you have not
given us much information on that!
> -Justin
> 
>> Could you tell me any suggestion
>> Thanks in advance.
>> 
>> 
>>      >
>>      > Could you tell me, did I miss something to use
>>      > Any suggestions would be appreciated
>>      > Thanks in advance
>> 
>> 
>> 
>> ------------------------------------------------------------------------
>> 
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
>or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------