Re: [AMBER] External forces

From: Josh Berryman <>
Date: Tue, 8 Dec 2015 11:12:00 +0100

Hello Jack,

the forcefield file is not what you are after.

The section or the manual on NMR restraints should give you instructions
for setting up a positional restraint, these are commonly used for
pulling-type simulations. AFAIK for moving restraints, the normal
procedure is just to retart the simulation every few nanoseconds with the
restraint minimum at a new position, by defining a relatively soft
potential and by making only small jumps then you can avoid jagged lines in
your output data.


On 7 December 2015 at 18:29, Jack Shepherd <> wrote:

> Hi all,
> I am interested in applying external forces to a length of DNA (eg at the
> terminal base pairs to stretch the molecule), but not exactly sure about
> it. Is it simply a case of suitably editing the forcefield file, or is
> there more to consider?
> Thank you in advance
> Jack Shepherd
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Received on Tue Dec 08 2015 - 02:30:03 PST
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