> On Aug 8, 2014, at 7:12 AM, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
>
> Dear amber-ites (and particularly the pmemd.cuda developers),
>
> I have generated a prmtop with chamber. Subsequently, I modified the prmtop
> with parmed.py to change the LJ parameters in accordance to the NBFIX
> corrections (for sodium - carboxylate interactions) that are now
> recommended for the CHARMM protein force-field (v36).
>
> sander & pmemd have no problem running with this modified prmtop, but
> pmemd.cuda gives the following error:
>
> CUDA (GPU): Prmtop appears to contain modified off-diagonal elements for
> VDW A coef.
> GPU code does NOT support such force field modifications.
> Found Aij = 61596.8299420842 expected
> -96740.2772678219
> i = 36 j = 3 Matrix element = 633
>
> (I've confirmed that pmemd.cuda runs fine with the prmtop prior to the
> NBFIX correction.)
> This is NOT the most recent pmemd.cuda version (I don't have access to that
> yet), I used
> Version 12.3.1
>
> Can I confirm that it is thus not possible not to use the NBFIX corrections
> in combination with pmemd.cuda?
> And, are there any plans to support this in the future? (Or is it already
> supported in a more recent pmemd.cuda version?)
It is already supported by Amber 14.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 08 2014 - 06:30:02 PDT
