On Fri, 2015-01-30 at 15:11 +0000, Ilyas Yildirim wrote:
> To MODERATOR: I've sent the same email today early morning with some
> attachments, but the size of the attachments were too big, which required
> the moderator to decide to post or not. I am re-sending the email without
> the attachments; thus, please discard and do not send the previous email
> to the list.
>
> Dear Jason, Scott, Dave, and Ross,
>
> I have been reading this thread since Rosie described the problem with the
> energies coming out different at each new calculation. Scott and Jason were
> talking about the problem arising due to the GB model, or the method it is
> being used by cuda. So, I provided Rosie with a new prmtop/inpcrd input set
> directly created with ff12SB force field. The new set seems to work fine. The
> previous one was created with new frcmod/lib files loaded over ff12SB. The new
> frcmod has new atom types in it, and it seems that those are the ones causing
> the problem (though it is not clear yet to me why energies are different at the
> end). You can check out the prmtop.notworking and prmtop.working from the
> following address:
>
> http://www-wales.ch.cam.ac.uk/rosie/new_input/
The two prmtops are exactly the same:
swails.batman $ diff prmtop.notworking prmtop.working
swails.batman $
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 30 2015 - 10:30:02 PST
