There is at least one publication stating that it used 12-6-4 with pmemd:
DOI: 10.1021/acs.jctc.6b00173
On 01/31/2017 02:11 PM, Qinghua Liao wrote:
> It currently only supports sander and pmemd
> (both the serial and MPI versions) but not pmemd.cuda.
>
> copied from the manual (page 321)
>
> On 01/31/2017 01:53 PM, Marcelo Andrade Chagas wrote:
>> Hi,
>>
>> Lj 12-6-4 is avaliable for sander, sander.MPI, and not by pmemd or pmemd.MPI
>>
>> Regards
>>
>> No dia terça-feira, 31 de janeiro de 2017, Ross Walker <
>> ross.rosswalker.co.uk> escreveu:
>>
>>> Hi Andreas,
>>>
>>> No, unfortunately GPU code was never written for the 12-6-4 LJ model so it
>>> is CPU only I am afraid. However, it's strange that the GPU code would just
>>> run with it. At the time 12-6-4 was added to PMEMD a check should have been
>>> added to the GPU startup code to quit if 12-6-4 was detected. The authors
>>> of the 12-6-4 model should check this.
>>>
>>> All the best
>>> Ross
>>>
>>>> On Jan 31, 2017, at 04:40, Andreas Tosstorff <
>>> andreas.tosstorff.cup.uni-muenchen.de <javascript:;>> 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 Is this information outdated or is pmemd.cuda just ignoring lj1264=1?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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--
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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Received on Tue Jan 31 2017 - 05:30:06 PST
