VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Mar 17 2004 - 11:39:15 CST

There is not a number limit. I have generated systems with millions of
atoms.

Can you be more specific about the errors?
Does solvate complain?
Are you starting off with a psf and pdb file?

It is easiest to start solvate with a pdb and psf file. Having said that
generating the psf file from your original pdb file may be a little
difficult but certainly doable.

Regards
Brian

 On Wed, 10 Mar 2004, Satyavani Vemparala
wrote:

>
> Hello:
>
> I have a PDB file (with water already present) of ~150000 atoms. This is
> lipid bilayer file, and iam trying to add more water to this bilayer.
>
> In the past i have been successfully able to do this with the help of some
> helpful suggestions by this forum, by using "-minmax" option.
>
> But with this file, i have been having problems, and number of waters
> coordinates are set to zero after i run the solvate script.
>
> Is there a limit on number of atoms, solvate can handle?
>
> any suggestions?
>
> Thanks
> Vani
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************