[gmx-users] pdb

Xavier Periole x.periole at chem.rug.nl
Wed Jul 14 14:28:15 CEST 2004

Dinesh Pinisetty wrote:

>Hi everyone,
>           I have taken one molecule with 23 atoms from a pdb file of
>Glycerol and have written a code in such a way that it translates into
>multiple molecules.I have created 8 molecules and then run md
>simulations.When I run the mdrun finally it run but at the end it is
>displaying step9.pdb,step8.pdb etc.When I checked with ngmx just for
>molecules it was not in the box but again when I used genbox and added
>water molecules I got the molecule in center with water molecules around
>but when I tried to animate it was not working,I think it did not run the
>simulation.Is it the problem with the pdb file I am using, as the
>co-ordinates are just translated in one direction.Is it the indication that
>when simulation did not run properly that we get step7.pdb ,step8.pdb
>etc.Now with this problem how can run the simulation,Can anyone help me in
>getting pure Glycerol pdb file with residues in residue data
> please let me know this.
>Thanks in advance.......
There are many steps between the pdb2gmx to the mdrun !! Many of them can
be the source of your error.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

More information about the gromacs.org_gmx-users mailing list