Hi, Meng
I suggest to use the distance from the substrate to the COM of the channel
exit, if you are trying to use PMEMD in GPU,
you can try the NFE module, in which you could define the COM restraint in
&pmd to umbrella sampling,
Here you can check the details in this tutorial
http://ambermd.org/tutorials/advanced/tutorial31/
Best
Feng Pan
On Thu, Apr 13, 2017 at 5:27 AM, 吴萌 <wumeng.shanghaitech.edu.cn> wrote:
> Dear All,
>
> I am trying to use the AMBER umbrella sampling method to get the free
> energy of transfer profile for a substrate molecule through a channel
> protein. And I have referred https://github.com/callumjd/
> AMBER-Umbrella_COM_restraint_tutorial , but several problems have trapped
> me due to my system is different. 1) If I put one substrate molecule close
> to the protein channel entrance, how can I define its location, I mean such
> as Z=0(need it to get r2=? in the pull.RST); 2) Also the distance restraint
> file, I use igr1=substrate atom number, how should I difine igr2=? use
> residue near the protein channel exit? If yes, use one or several?
>
> Any suggestions would be greatly appreciated.Thank you in advance!
>
> All the best,
> Wu Meng
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 13 2017 - 13:30:02 PDT
