Re: SMD with force applied to two seperate molecules

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Thu Aug 13 2009 - 10:48:44 CDT

or, by the way, have you looked at the constantForce option? that might help.

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node18.html

On Thu, Aug 13, 2009 at 11:24 AM, Roman Petrenko<rpetrenko_at_gmail.com> wrote:
> to my understanding imaginary SMD point is the COM of the group of all
> SMD-atoms.
>
> why do you need to apply a force to both molecules? fix one and move the other.
>
> if you indeed need to pull two molecules, each in opposite direction,
> the only solution is to use tcl-forces script (not for beginners).
>
> On Tue, Aug 11, 2009 at 11:09 AM, Elia Zumot<enz1+@pitt.edu> wrote:
>> Dear NAMD users,
>>
>> I'm doing SMD with CV for a dimer protein (each has its own substrate) by
>> applying force to the two substrates (about 20 A apart, using a single
>> reference file) to force them out of their binding pocket.
>> I got two questions:
>>
>> 1)Is the COM (where force is applied) in this case an imaginary point in
>> space halfway between the two molecules or are there two COMs?
>>
>> 2) Is it possible to get the trajectory of Force (or PMF) applied to each
>> molecule alone? (or alternatively apply two different forces to both
>> substrates)
>>
>> I am also asking this because only one of the two molecules moves but not
>> the other (whereas at higher unrealistic velocities both move).
>>
>> Thanks in advance
>>
>> Elia
>>
>>
>
>
>
> --
> Roman Petrenko
> Physics Department
> University of Cincinnati
>

-- 
Roman Petrenko
Physics Department
University of Cincinnati

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