From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Nov 14 2016 - 15:59:07 CST
On Mon, Nov 14, 2016 at 4:17 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
>
>
> 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”.
>>
>
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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 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
>
> 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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