question about Steered Molecular Dynamics

From: Oleksii Zdorevskyi (zdorevskyi_at_bitp.kiev.ua)
Date: Wed Feb 15 2017 - 08:38:22 CST

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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