Hi Rajarshi,
Dave is correct the GPU code only supports distance based center of mass restraints. Angle and dihedral COM restraints are not supported.
The only option right now is to use the CPU code.
All the best
Ross
> On Mar 19, 2018, at 06:39, Rajarshi Roy <phd1701171011.iiti.ac.in> wrote:
>
> Dear Sir,
> I make this restraint file using cpptraj. Is there any alternative way of
> writing it or It is not possible to run in cuda?
>
> On Mon, Mar 19, 2018 at 12:22 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Thu, Mar 15, 2018, Rajarshi Roy wrote:
>>>
>>> I am trying do an umbrella sampling of nucleic acid. One of my restraint
>>> co-ordinate is cpd angle (pseudo- dihedral angle ), for that I need to
>>> restraint center of mass of four group of atoms. I am little bit confuse
>>> how to choose the iat value. In the manual I found that it should be
>>> negative, but it is not running in cuda. Here is my restraint file,
>>
>> I'm pretty sure pmemd.cuda only supports COM distance restraints, and
>> not the corresponding angle or dihedral restraints.
>>
>> Hence the "igr3" and "igr4" namelist values are not legal ones.
>>
>> [Please, someone correct me if I'm wrong, or out of date here!]
>>
>> ....dac
>>
>>
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>
>
>
> --
>
> with regards
> Rajarshi Roy
>
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
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Received on Tue Mar 20 2018 - 08:00:02 PDT
