RE: SMD on a group of atoms: Confusion

From: Blake Charlebois (bdc_at_mie.utoronto.ca)
Date: Fri Sep 03 2004 - 05:41:24 CDT

Vani,

Most (if not all) available approaches to holding atoms fixed are described
here:
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 http://www.ks.uiuc.edu/Training/SumSchool/

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?

Blake

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Vani Krishna
Sent: September 1, 2004 11:48 AM
To: namd-l_at_ks.uiuc.edu
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
helpful.

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
{x2,y2,z2}?

Thanks
Vani

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