VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 07 2020 - 14:20:02 CST

Hi,
  I'd suggest asking NAMD SMD tutorial questions on NAMD-L, you are more
apt to obtain assistance there than here on VMD-L.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 02, 2020 at 10:27:48AM +0530, surya narayanan chandrasekaran wrote:
> 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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/