RE: SMD on a group of atoms: Confusion

From: Blake Charlebois (
Date: Fri Sep 03 2004 - 05:41:24 CDT


Most (if not all) available approaches to holding atoms fixed are described
1) "6.1.2 Fixed atoms parameters" in the NAMD manual (version 2.5)
2) "6.6. Applied Forces and Analysis" in the NAMD manual (version 2.5)
3) lectures and tutorials at

Which approaches have you tried so far?

Is it critical that the COM be fixed, or would it suffice to fix or
harmonically constrain part of the protein?


-----Original Message-----
From: [] On Behalf
Of Vani Krishna
Sent: September 1, 2004 11:48 AM
Subject: namd-l: SMD on a group of atoms: Confusion

Hello all:

Thanks for all the previous replies regarding patches
on protonation .

I have a question regarding doing SMD simulations on a
group of atoms. From the User guide, i understand that
when i want to 'pull' a group of atoms, i can specify
the group by changing occupancy column. What iam
confused about is that how the center of mass of the
protein is held fixed? Iam trying to pull a molecule
from inside of the protein into solution and when i do
this, the whole system moves, which is obvious as I
have not fixed the protein COM. Iam new to SMD and any
suggestions/references in this regard would be most

Is there a way to perform multiple SMD at the same
time? i.e, pull group A in {x1,y1,z1} and group B in


Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:51 CST