Re: TCL Scripting for Force Calculations

From: Allen, Caley R (caley.allen_at_chemistry.gatech.edu)
Date: Mon May 02 2016 - 14:08:17 CDT

Hello Jrme,

Thank you for the quick response.

I have flagged specific atoms in the PDB file by altering the beta column, to say a 1 and all other atoms to 0. Then in the namd gconf file I have used fixedAtoms. So I am familiar with using flags in the PDB file.

How would I incorporate that idea into something like the following (this is an exert from the smdforce.tcl script I have used before)?:

# Atoms selected for force application

set id1 [atomid A 1 CA]
set grp1 {}
lappend grp1 $id1
set a1 [addgroup $grp1]

set id2 [atomid A 43 CA]
set grp2 {}
lappend grp2 $id2
set a2 [addgroup $grp2]

I am attempting to minimize the number of lines changed in the code I am currently using.

Sorry if I am missing the message.

Cheers,

Caley

Caley Allen, Ph.D.

Postdoctoral Fellow

The Georgia Institute of Technology

Hernandez Research Group

________________________________
From: Jrme Hnin <jerome.henin_at_ibpc.fr>
Sent: Monday, May 2, 2016 12:37 PM
To: Namd Mailing List; Allen, Caley R
Subject: Re: namd-l: TCL Scripting for Force Calculations

Hi Caley,

This sounds like it would be easier to do with the collective variables module. You can define your sets of atoms by flagging them in a PDB file, or based on residue and atom names, or with a GROMACS-format index file if you happen to use those. Then steered MD is implemented as a moving harmonic bias. If you want a custom algorithm, you can Tcl-script your own colvar bias:
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-720006.7

Best,
Jerome

On 2 May 2016 at 17:48, Allen, Caley R <caley.allen_at_chemistry.gatech.edu<mailto:caley.allen_at_chemistry.gatech.edu>> wrote:

Good evening NAMD Community.

I am familiar with and have executed steered molecular dynamics simulations before using single atom sites for the anchor cite and pulling cite. I have a TCL script written for use with NAMD to do just this. Currently I have been trying to do something a little different. I am currently trying to steer a polypeptide from a surface by using center of masses instead of single atoms (using and adaptive SMD). I know how to determine the center of masses for the surface, and for the polypeptide. However, I do not know how to incorporate these center of masses into the TCL script. I know NAMD provides TCL scripting interface in a limited manner. I have tried to use the "TCL Forces and Analysis" webpage for help, but I am not getting anywhere. I know I can use addgroup, but how do I list the surface (and like wise for the polypeptide)?

Maybe I am missing something simple.

Any help would be greatly appreciated.

Thank you in advance.

Cheers,

Caley

Caley Allen, Ph.D.

Postdoctoral Fellow

The Georgia Institute of Technology

Hernandez Research Group

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