AMBER Archive (2002)

Subject: amber trajectory

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Dec 17 2002 - 23:16:14 CST

Hi amber-users,

I have a small trajectory generated with amber7 on SGI/IRIX (octane)
machine. It is a cubical water box (L=20A) and I've run NVT dynamics
using PBC. When I load the .crd file into VMD the bonds seem to be
extremely stretched. However from the output it seems that there is
nothing really wrong with the energy or with the run itself. I wonder if
this is an artifact of the PBC visualisation in VMD?

Thank you and Happy holidays!

Ioana

****************************************************************************
* Ioana Cozmuta, PhD * *
* NASA-AMES Research Center * "Gravitation can not be held responsible*
* Mail Stop 230-3 * for people falling in love" *
* Moffet Field,CA 94035 * *
* phone: (650) 604-0993 * Albert Einstein*
* fax: (650) 604-0350 * (1879-1955) *
****************************************************************************