AMBER Archive (2002)

Subject: rms and watershell (in ptraj)

From: dkon_at_email.arizona.edu
Date: Wed Feb 20 2002 - 18:54:58 CST

Dear folks,

I'm trying to analyze water penetration into a cavity during the simulation
(periodic box, constant-pressure, 300K run). I use the watershell command
in ptraj to keep track of close waters. I'm concerned, however, that something
is fishy because if I perform the watershell command on my trajectory with
and without an rms fit (to take out translation and rotation) I get completely
different results. But rms should not affect interatomic distances within
any given frame. I've checked that by monitoring distances between selected
atoms in the trajectory with and without rms fit. It appears that the distances
within the protein are well-preserved by rms, but distances between water
molecules and protein atoms are not (or not always). Here are my questions:

1) During rms fit, is the corrective translation/rotation applied to sovent
as well as the solute?

2) Is there some water imaging problem that is created by rms fitting?

3) Are there any known bugs/subtleties with watershell that I should be
aware of?

Thank you in advance,
Dmitry