Hi Jason,
You have added code in Amber to raise error message when using 12-6-4 with GPU simulation, right?
And I think from Amber14 both sander/sander.MPI and pmemd/pmemd.MPI have supported 12-6-4 simulation. In default the 12-6-4 potential is turned off in the former version(s), but now Amber can detect the C4 terms based on the prmtop file automatically to determine whether 12-6-4 or 12-6 potential should be used. are these statements right?
Kind regards,
Pengfei
> On Feb 2, 2017, at 8:27 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> I'm a little late to the party here, but if you needed the added
> performance of GPUs for the 12-6-4 model, OpenMM supports it (using native
> Amber prmtop and inpcrd files).
>
> And parmed has an "OpenMM" command that will read basic sander/pmemd input
> files and generate NetCDF trajectories (with a sander-like set of
> command-line options) for the small subset of functionality that is
> supported by that interface (for the most part, just basic MD with
> optionally some simple restraints).
>
> HTH,
> Jason
>
> On Tue, Jan 31, 2017 at 4:40 AM, Andreas Tosstorff <
> andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
>> Hi all,
>>
>> I want to run some REMD simulations with a peptide/Zinc system.
>>
>> I wanted to use th 12-6-4 LJ-Type Nonbonded model.
>>
>> I generated the parm7 and crd files according to the manual and ran my
>> first simulation using pmemd.cuda.
>>
>> lj1264 is set to 1 and the simulation ran without any errors, however it
>> did not produce the expected outcome, meaning that Zn2+ would bind to a
>> HIE residue in its proximity.
>>
>> I read in the manual that lj1264 is not supported by pmemd.cuda.
>>
>> Is this information outdated or is pmemd.cuda just ignoring lj1264=1?
>>
>> Should I rather use 12-6 LJ-Type with pmemd.cuda?
>>
>>
>> Kind regards,
>>
>>
>> Andreas
>>
>>
>> --
>> M.Sc. Andreas Tosstorff
>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
>> Department Pharmazie
>> LMU München
>> Butenandtstr. 5-13 ( Haus B)
>> 81377 München
>> Germany
>> Tel.: +49 89 2180 77059
>>
>>
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>>
>
>
>
> --
> Jason M. Swails
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Received on Sat Feb 04 2017 - 14:30:03 PST
