From: Jim Phillips (
Date: Mon Dec 03 2001 - 11:14:50 CST


This option is currently available only for water. (Personally, I've
always felt this would be VMD's job, since wrapping molecules in NAMD
output looses information.) If you wanted to change this, look for
"wrapWater" in CollectionMgr.C to see how it's done now. There is
currently no code for identifying individual molecules besides water.


On Mon, 3 Dec 2001, Reuter Nathalie wrote:

> Dear all,
> I am a new user of NAMD (I used Charmm til now) and I try to simulate
> boxes of mixed solvent (mixture of water and trifluoroethanol-TFE at
> first). I would like to 'wrap' the TFE molecules at the end of each
> simulation but it seems that I can 'wrap' only the water molecules with
> the 'wrap water' option in the configuration file. Is there in NAMD such
> an option for other kind of particles than water ? Or should it be added
> in the code ? If it is the case, I would be more thankful if you could
> indicate me in which source file.
> Thank you for your help,
> Nathalie Reuter
> --
> Nathalie REUTER, PhD
> U.410 INSERM
> Faculte de medecine Xavier Bichat
> 16, rue Henri Huchard
> BP 416
> 75870 PARIS Cedex 18
> tel : (33)
> fax : (33)