[gmx-users] Reg: Adding multiple molecules

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:
> Hi justin
> 
> if genbox is not able to find sufficient space then why should one 
> calculate number density for the given box dimension?.similarly the  the 

Just because you can calculate a certain number density does not necessarily 
mean that the algorithm genbox is using can produce such a configuration.  It 
inserts molecules randomly, so you may be able to find a magical value of -seed 
for which this will work.  The simpler approach is what I suggested earlier.

> number of molecules are not getting updated in the molecules section of 
> the topology file when inserting multiple molecules using the genbox 
> command. everytime i need to update it manually.is <http://manually.is> 
> there a way to update it automatically?
> 

The topology will only be updated automatically when adding water.  Otherwise, 
you have to do it yourself.

-Justin

> Regards
> Vinoth
> 
> On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     vinothkumar mohanakrishnan wrote:
> 
>         Hi all
> 
>         I have a diffculty in adding multiple molecules of hexane to my
>         box. my box size is 4.72*2.36*2.36 (nm) according to my number
>         density calculations the box should fit 124 molecules of hexane
>         whereas it adds only 76 molecules to the box below is my
>         command. i had evev tried with -try command but without sucess.
> 
>         genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o
>         hexane-multi.gro -nmol 124 -seed 1268
> 
> 
>     If you're not getting all the molecules you want, then genbox is
>     unable to find sufficient space for them.  Try a larger box, then
>     equilibrate.
> 
>     -Justin
> 
>         Regards
>         Vinoth
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================