regarding your qusteion on restraints
the ntr = 1 will turn on position resratints on the atom specified under
GROUP in the input file .it works just like a spring attached to each atom
which will pull the atom back if displaced 9 via harmonic potential )
or u can use BELLY option which will make the force on the atoms equal
to zero in each step but this can lead to some problems in periodic
boundary simulations
On Sat, Jun 23, 2012 at 11:40 AM, vishal kumar Jaiswal <vishal3990.gmail.com
> wrote:
> if you want your trajrctory with the protein in center you can use some
> residues to define a center and then image back everything using ptraj.
>
> ptraj input file>
>
>
> trajin your-trajrctory-file
> trajout another-trajrctory-file filetype box
> center :a-b (a to b are numbers of residus to consider in center of
> geometry)
> image
> go
>
> use this input file as
> ptraj your-topology-file ptraj-input-file
>
>
> On Sat, Jun 23, 2012 at 11:04 AM, Adam Jion <adamjion.yahoo.com> wrote:
>
>> Hi,
>> How does restraining a residue work in Amber?
>> For example, if I have a giant protein that traverse across a wall of a
>> simulation box under periodic boundary conditions, and if I were to
>> restrain the protein to these initial coordinates, will the simulation box
>> be able equilibrate under NPT simulation?
>>
>> Regards,
>> Adam
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sat Jun 23 2012 - 03:00:03 PDT
