[gmx-users] Re: solvation

[Jamie Seyed]

Hi Justin,
Thanks for comments,
On Thu, Aug 13, 2009 at 8:21 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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?

my command is:
genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 -nmol
1 -ci insert.gro
I also tried
genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 -nmol
1 -ci insert.gro -try 100
by using 20,30,40...,100 but each time was the same. (I also did it without
shell command but no success)

>
> (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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