spoel at xray.bmc.uu.se
Wed Jul 14 08:04:58 CEST 2004
On Wed, 2004-07-14 at 04:38, 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
If you start by minimizing the energy of one molecule (and verify it
keeps it structure) you can thereafter use genconf to get multiple
molecules, and genbox to solvate them.
> please let me know this.
> Thanks in advance.......
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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