[gmx-users] Re: solvation

[Justin A. Lemkul]

Jamie Seyed wrote:
> Hi all,
> Thanks for your comments. Actually as Vitaly mentioned I am still try to 
> visualize the gro-file made by genbox. I found out for any number that I 
> use for "-nmol ? -ci insert.gro" after some iterations and upto these 
> values:
> Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
> System total charge: 0.000
> I get segmentation fault. In fact cut-off values from 0.1 in the case of 
> -nmol 0, jumps to 0.45 in the case of -nmol 1 and then it gives me 
> segmentation fault. The only way to get rid of it is put -nmol 0!
> Now my questions are:
> (1) What can be wrong in my insert.gro file. Does it matter the 
> coordinates of 1 molecule that I obtained from spc216.gro file?? The 
> format is the same.

Can you post your exact command line?

> (2) This command will try to add water where? In the same coordinates as 
> insert.gro??

 From genbox -h:

"3) Insert a number (-nmol) of extra molecules (-ci) at random positions. The
program iterates until nmol molecules have been inserted in the box. To test
whether an insertion is successful the same VanderWaals criterium is used as
for removal of solvent molecules. When no appropriately sized holes (holes
that can hold an extra molecule) are available the program tries for -nmol *
-try times before giving up. Increase -try if you have several small holes to
fill."

-Justin

> What is your suggestions?? Many Thanks in Advance/Jamie
> 
> On Thu, Aug 13, 2009 at 5:25 PM, Vitaly V. Chaban <vvchaban at gmail.com 
> <mailto:vvchaban at gmail.com>> wrote:
> 
>     Tsjerk,
> 
>     I understood the situation in such a way that MD was not run at all,
>     so Jamie visualizes *gro* file obtained with *genbox*...
> 
>     Jamie,
>     didn't you look at this: http://www.ime.unicamp.br/~martinez/packmol/
>     to prepare your system?
> 
> 
>     Vitaly
> 
> 
>      >
>      >> Thanks for the answer. When I said far away means my pore was in
>     one corner
>      >> of vmd window and the water molecules in opposite corner (almost).
>      >
>      > Did I miss something or did neither Vitaly nor Justin reply "Are you
>      > perhaps seeing the effect of periodic boundary conditions?".
>      >
>      > Tsjerk
>      >
>      > --
>      > Tsjerk A. Wassenaar, Ph.D.
>      > Junior UD (post-doc)
>      > Biomolecular NMR, Bijvoet Center
>      > Utrecht University
>      > Padualaan 8
>      > 3584 CH Utrecht
>      > The Netherlands
>      > P: +31-30-2539931
>      > F: +31-30-2537623
> 
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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