[gmx-users] using 'genbox' for adding solvent

[Justin A. Lemkul]

Amit Choubey wrote:
> I still want to suggest that segmentation fault doesn't occur due to 
> large no. of insertion molecules the reason being that i, once tried to 
> insert only 1 molecule and it came up with seg. fault again . I am very 
> sure that i have space for atleast some(>1) no. of water molecules.
> 

Which version of Gromacs are you using?  There was a bug in genbox 4.0.3, but 
was fixed prior to 4.0.4.

-Justin

> Amit
> 
> On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Amit Choubey wrote:
> 
>         Hi everyone,
> 
>         I have been trying to insert a fixed no. of water molecules in
>         my system. I first tried the -cp -cs options and could insert
>         some water molecules. But I still need to insert  few more water
>         molecules and for that i tried using the -nmol -ci option. I
>         made a file named "insert.gro" which has a single water molecule
>         with the right volume associated with it. But this option gave a
>         segmentation fault and i am not sure why its doing that? May be
>         there's not enough space for additional water but it should not
>         give a segmentation fault for that reason. Is there something
>         wrong with my idea?
> 
> 
>     A segmentation fault with this approach generally indicates that the
>     requested number of inserted molecules will not fit.
> 
>     Alternately, you can try -cs spc216.gro -maxsol (your number)
> 
>     If the second approach also fails, I would think that would be
>     strong evidence that what you're trying to do won't work.
> 
>     -Justin
> 
>         The insert.gro looks like the following
> 
>         H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984
>          3
>            1SOL     OW    1    .130    .128    .113
>            1SOL    HW1    2    .037    .126    .150
>            1SOL    HW2    3    .131    .089    .021
>           0.31034   0.31034   0.31034
> 
>         I also tried various other box (larger) sizes for this but it
>         didnt help.
>         Thank you in advance.
> 
>         Amit
> 
> 
>         ------------------------------------------------------------------------
> 
>         _______________________________________________
>         gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://lists.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
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     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
> 
>     ========================================
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

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

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