On Thu, Dec 16, 2010 at 2:22 PM, Xiao Ju Zhang <xiaojuzh.gmail.com> wrote:
> Dear all,
>
> Does anyone happen to use AMBER forcefields in NAMD? Does NAMD give same
> initial energy (bond, angel, and dihedral ect.), as it use the same input
> generated by AMBER and AMBER forcefields?
>
> I am trying to simulate RNA molecule with NAMD using the initial inputs
> generated from AMBER, and the forcefield for the simulation is AMBER
> forcefield 99. In the user guide, there is a chapter clearly instructs how
> to do it. In the Caveat section, the guidance mentions that " Polarizable
> parameters in AMBER are not supported. " What I am not sure is, does this
> mean that even with the same input and AMBER ff99 parameters, the starting
> energy is somehow different than it should be in AMBER?
>
FF99(SB) is not polarizable, so this should not apply here. I know that
there has been someone working on comparing NAMD and Amber, and he has
indeed gotten them to agree quite well. Perhaps he will respond here. You
have to make sure that certain conditions are the same, especially PME
settings (i.e. make sure you have the same grid, gaussian widths, same
cutoff, etc.)
Hope this helps,
Jason
> Any comment or suggest will be very welcome.
>
> Thank you in advance, and happy holidays!
>
> Ju
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 16 2010 - 12:00:03 PST
