[gmx-users] Disappear my solution

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 28 14:55:34 CEST 2008

Morteza Khabiri wrote:
> Dear
> I have a box with 2 different kind of solution and one protein. Actually,
> I minized my box in each step which i add matter to box. After
> minimization of my system I run it for 10 ns. unfortunately after 1.3 ns
> one of my solution dissapear. eg, I have hexan organic solvent, water and
> protein, after this time the hexan dissapear. everything is ok. log file
> enrgy file and .. are ok . I repeated my run for 3 times but in each time
> after 1.3 ns my hexan dissapear. Please guid me what could be the problem.
> I attache my grompp file also.

What do you mean by "disappear?"  How are you making this determination?  What 
is written to the .gro file?  Are you extracting coordinates from a trajectory, 
visualizing with VMD (or some other program)?

I find it highly unlikely that mdrun is forgetting to write a specific component 
of your system.  Please provide more details as to your procedure (i.e., answer 
the questions I asked above).


> thank you very much for your help
> Yours,
> Morteza
> ------------------------------------------------------------------------
> _______________________________________________
> 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


More information about the gromacs.org_gmx-users mailing list