Hi, James
An option is that you can use the module ncsu_smd to run the SMD with your
distance restraint. At the same time you can apply your normal distance
restraint with nmropt, there will be no conflict.
The ncsu_smd currently only works with SANDER, but there will be an update
that it will be implemented to pmemd & pmemd.cuda soon.
Best
Feng Pan
On Wed, Jun 8, 2016 at 6:39 AM, James Murdock <james.murdock.86.gmx.com>
wrote:
>
> Dear AMEBR users,
> In Amber16, I tried to run a simulation with 3 nmropt restraints: two
> normal
> distance restraints and one distance restraint to be used with the
> Jarzynski
> Relationship (jar=1 in the mdin file). However, pmemd dies with:
> jar option running
> In Jarzynsky runs, there must only one restrain, stopping program
> Can we expect an update where the above situation is possible? Maybe a
> flag
> in the .RST file to indicate which restraint is to be used with the
> Jarzynski Relationship?
> Regards,
> JM
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Received on Wed Jun 08 2016 - 09:30:02 PDT
