VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Wed Jan 01 2020 - 22:57:48 CST

Hi all,
          I was doing an SMD tutorial. But while doing for my system in the
water there are some doubts:
1> How to specify the selection of residue. for example, it uses the below
code. How can I implement between residues?

set id1 [atomid YP2 0 C1]
set grp1 {}
lappend grp1 $id1
set a1 [addgroup $grp1]

If I use the normal selection resname then how to specify the constraint
points?
What is the meaning of constraint points ? is it really constraint or
pulling direction between one residue and another?

set c1x 0.0
set c1y 0.0
set c1z 0.0

set c2x 0.0
set c2y 0.0
set c2z 13.0

is the constraint always needs to specific between one atom and another
atom ?? I am interested in graphene exfoliation and this paper says (
10.1021/acs.jpcc.5b03217 <http://dx.doi.org/10.1021/acs.jpcc.5b03217>)
constrained one graphene sheet then pulled another graphene sheet through
an atom. how can I specify the pulling direction?

During the SMD simulation, one needs to keep "fixed atom on" and Langevin
temp on? The tutorial always talks about the vacuum system mine is in water
so I am confused ?? 

-- 
Warm regards,
Surya