From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Feb 15 2017 - 17:11:42 CST
Hi Oleksii,
You can perform SMD in a very flexible way if you define it as a set of
moving harmonic restraints on collective variables.
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-720006.4.1
The details of which variable is most relevant depends on your system, but
they are likely to be distances or distance vectors between atoms and fixed
positions in space (specified as dummy atoms with the dummyAtom keyword).
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-200005.1.1
Here is a first idea of what the colvars input might look like:
colvar {
name vec1
outputAppliedForce
distanceVec {
group1 { dummyAtom (42, 42, 42) } # reference position in space (e.g.
initial position)
group2 { atomNumbers 1 2 3 } # atoms to pull in molecule 1
}
}
colvar {
name vec2
outputAppliedForce
distanceVec {
group1 { dummyAtom (42, 42, 42) } # reference position in space (e.g.
initial position)
group2 { atomNumbers 4 5 6 } # atoms to pull in molecule 2
}
}
harmonic {
colvars vec1 vec2
forceConstant 42
centers (0, 0, 0) (0, 0, 0) # initial values of the vector distance
targetCenters (10, 10, 10) (10, 10, 10) # final values
targetNumSteps 1000000 # number of timesteps for the pulling process (can
be longer than one single NAMD run)
outputAccumulatedWork
}
Best,
Jerome
On 15 February 2017 at 08:38, Oleksii Zdorevskyi <zdorevskyi_at_bitp.kiev.ua>
wrote:
> Dear NAMD developers,
>
> I would like to ask you a question about Steered Molecular Dynamics in
> NAMD: Can we pull several atoms in different directions at the same time?
>
> I use NAMD for studying the processes of DNA unzipping and DNA stretching.
> To perform this simulations it is required to pull in the same time two
> atoms from different strands in the opposite directions (unzipping) or
> to fix both strands from the one end and to pull this strands along the
> helix axis from the other end (stretching).
>
> In NAMD Tutorial (
> http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html ) it is shown
> how to pull one atom of a protein when one other atom is fixed. So that we
> have one SMD atom, one fixed atom and one vector of pulling direction.
> Could you tell me please if it is any possibility in NAMD to have several
> SMD atoms, several fixed atoms and several vectors of pulling direction
> in the same SMD simulation?
>
> I looked for the similar questions through the internet but neither
> Google, nor NAMD-L do not have any discussion about it. Thank you in
> advance.
>
> Yous sincerely,
> Oleksii Zdorevskyi
>
>
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