Re: SMD restraints

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Nov 14 2016 - 15:17:59 CST

On Mon, Nov 14, 2016 at 4:14 PM, Allen, Caley R <
caley.allen_at_chemistry.gatech.edu> wrote:

> Greetings NAMD experts.
>
>
>
> I was browsing through the mail list, in an effort to find a solution to a
> problem when I stumbled upon a post from Feb. 29, 2012. The interesting
> part (to me) reads as follows (Axel wrote the response in black):
>
>
>
> *What you say makes sense, but I want to compute the work done by the
> pushing*
>
> no. this is bad. you cannot change the force field.
>
> *force as I insert the peptide into the membrane (steered MD). Hopefully
> I'll*
> *get some free energy profile as a function of insertion depth. Hence I
> need*
> *the membrane to stay in place.*
>
> not quite. what you need is to have the steering force
> being applied to both, the center of mass of the *entire*
> membrane and the center of mass of the *entire* protein.
>
> restraining a few lipid molecules in space will not help.
> best case, it will artificially bend the membrane, worst
> case, it will just rip those out.
>
> in general, you should not worry too much about a little
> drift, after all you have periodic boundary conditions,
> and for a clean steered MD PMF on inserting a protein
> into a membrane, you need quite a bit of water in between.
>
>
>
> I am attempting to do something very similar – I would like to “pull” a
> ligand off of the bilayer leaflet via SMD at a constant velocity. I choose
> a steering atom in the ligand and an “anchor” atom in a lipid in the
> bilayer. And the result was an impressively significant bending of the
> bilayer. It was pointed out in the passage above to use “the center of mass
> of the **entire** membrane, and the center of mass of the **entire**
> protein”.
>
>
>
> My question is how; how do you make the selection for the “center of mass
> for the entire membrane/protein”?
>

By defining a group and then use its COM and apply forces to it:
http://www.ks.uiuc.edu/Research/namd/2.12b1/ug/node50.html

>
>
> NAMD’s implementation of tcl is limited. For example currently in the
> smdforces.tcl script I make the atom selections for the force application
> as follows:
>
>
>
> set id1 [atomid A 1 CA]
>
> set grp1 {}
>
> lappend grp1 $id1
>
> set a1 [addgroup $grp1}
>
>
>
> Then similarly for id2.
>
>
>
> Would using colvars be a solution?
>

It would be another solution to the same problem.

>
>
> I am unfamiliar with colvars, so any examples and/or guidance is much
> appreciated.
>

http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html

>
>
> Cheers and Best Wishes,
>
> C. Allen
>
>
>
>
>
>
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
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Personal: http://giacomofiorin.github.io/
Lab page: https://icms.cst.temple.edu/members.html
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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