From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Nov 14 2016 - 16:26:01 CST
One of the ways around it is to use a better collective variable. For hydrophobic entities, instead of using the position along the membrane normal as the reaction coordinate, you could for instance use coordnum, which is short for the coordination number, and measures the number of contacts between two groups of atoms.
-Josh
On 11/14/2016 03:02 PM, Giacomo Fiorin wrote:
On Mon, Nov 14, 2016 at 4:17 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>> wrote:
On Mon, Nov 14, 2016 at 4:14 PM, Allen, Caley R <caley.allen_at_chemistry.gatech.edu<mailto: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”.
One non-trivial issue here is that you should expect some degree of bending in the bilayer upon extraction, especially for a very lipophilic ligand (e.g. try with a lipid molecule). Bending would occur also with the full-membrane center of mass. This is a common problem with the calculation of free energies of insertion / separation in bilayers.
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
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-- 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<tel:%2B1-215-204-4213> Scholar: http://goo.gl/Q3TBQU 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 -- 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 Scholar: http://goo.gl/Q3TBQU 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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