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.
Josh
On 7 December 2015 at 18:29, Jack Shepherd <jws526.york.ac.uk> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 08 2015 - 02:30:03 PST
