[gmx-users] default group question
ruiqiao at glsn12.ews.uiuc.edu
Mon Nov 10 21:14:01 CET 2003
I checked my .top file, and the residue name there is
SOL/LOL/HOL instead of just SOL.
Beckman Institute, UIUC
On 10 Nov 2003, David wrote:
> On Mon, 2003-11-10 at 17:05, qiao rui wrote:
> > Hi, there:
> > I am doing a simulation in which I wish to monitor the diffusion
> > of water molecules in my system. To this end, I have the following
> > topology file:
> > ...
> > SOL 100
> > LOL 100
> > HOL 100
> > ...
> > SOL/LOL/HOL are all water molecules, I define their residue name
> > in such a way to distinguish the water molecules in different part of the
> > system.
> > In using Gromacs, I first find that the default group shows SOL
> > only, but not LOL and HOL (why?) To solve this, I defined an index file,
> > where LOL and HOL are defined. However, after I did an energy
> > minimization, the output .gro file has only SOL - the name of LOL and HOL
> > molecules was changed to SOL (all the LOL and HOL waters are still
> > their, but their name was changed to SOL somehow). Why is this happening?
> It uses the residue name in the topology. You can however stil use your
> index file.
> > Thanks a lot for your input.
> > sincerely,
> > Rui
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> David van der Spoel, PhD, Assist. 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users