From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Nov 15 2016 - 13:17:17 CST
Hi Caley, please respond to the mailing list.
The addgroup and addforce keywords are documented fairly clearly in my
opinion, so I guess what you're asking is how to test whether the code will
work as you expect.
I would recommend a simple test by computing the COM of those atoms in VMD
(see the doc for the measure command there) and then printing the same COM
with NAMD.
FYI, watch out for possible issues with PBCs and wrapping of atoms.
Giacomo
On Tue, Nov 15, 2016 at 2:04 PM, Allen, Caley R <
caley.allen_at_chemistry.gatech.edu> wrote:
> Thank you Giacomo for your answer.
>
> I have seen the websites before. If I may quickly ask, by defining a group
> and then use its COM and apply forces to, I would use the addgroup and list
> each atom number? So for instance the bilayer I would list atomids 129
> -37061? I just want to make sure I understand .
>
> Thanks again.
> Best wishes.
> Caley
>
>
>
> Sent from my Verizon, Samsung Galaxy smartphone
>
> -------- Original message --------
> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> Date: 11/14/16 4:18 PM (GMT-05:00)
> To: NAMD list <namd-l_at_ks.uiuc.edu>, "Allen, Caley R" <
> caley.allen_at_chemistry.gatech.edu>
> Subject: Re: namd-l: SMD restraints
>
>
>
> 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
>
> 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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