VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Sep 22 2015 - 18:18:00 CDT

A quick follow-up on that. Is the "periodicity" the same thing as the
"multiplicity" in the manual (i.e. the n in the cos (n*phi - delta) term)?
In that case, I am assuming n has to be adjusted for each one based on the
molecule at hand, correct?

Chitrak.

On Tue, Sep 22, 2015 at 7:06 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> Hi Christopher,
>
> Sorry for the late reply. I solved this issue, I basically had two NAMD
> executables by the same name which was creating confusion. I have it fixed
> now.
>
>
> I have a question though. When I do the "scan torsion", there is a "Open
> Torsion Explorer" button that is not there in the video tutorial. Could you
> tell me what it is supposed to be used for? I was trying to use its
> "Analyze trajectory" button, but nothing seemed to happen.
>
> The other question I have is, from the video it isn't clear to me how to
> proceed on the optimization. For example, in the video, one of the
> dihedrals was duplicated. How do I know which one to duplicate? Also, when
> the video showed changing the periodicities to 3, is that a default setting
> (more like the 0.09 charge on aliphatic hydrogens), or was it specific to
> the molecule being discussed in the example?
>
>
> Best regards,
> Chitrak.
>
> On Mon, Sep 14, 2015 at 9:34 AM, Mayne, Christopher G <
> cmayne2_at_illinois.edu> wrote:
>
>> Chitrak,
>>
>> From the Opt. Bonded, set the NAMD bin just as you would when trying to
>> perform the optimization. Open the TkCon (Extensions -> TkConsole) and
>> type the following:
>>
>> exec $::ForceFieldToolKit::BondAngleOpt::namdbin
>>
>> Please respond with the output from the tkcon
>>
>> Regards,
>> Christopher Mayne
>>
>>
>>
>> On Sep 11, 2015, at 8:26 AM, Chitrak Gupta wrote:
>>
>> > Hi there!
>> >
>> > I am working on the FFTK Bond optimization, and I got this error:
>> >
>> >
>> >
>> > ------------- Processor 0 Exiting: Called CmiAbort ------------
>> > Reason: FATAL ERROR: Pair interaction calculation is not supported in
>> CUDA version
>> >
>> > Charm++ fatal error:
>> > FATAL ERROR: Pair interaction calculation is not supported in CUDA
>> version
>> >
>> > ------------- Processor 0 Exiting: Called CmiAbort ------------
>> > Reason: FATAL ERROR: Pair interaction calculation is not supported in
>> CUDA version
>> >
>> > Charm++ fatal error:
>> > FATAL ERROR: Pair interaction calculation is not supported in CUDA
>> version
>> >
>> >
>> >
>> > I verified the NAMD binary I selected was namd2 (which is the CPU
>> version). Is there some other setting to get it to use the CPU version?
>> >
>> >
>> >
>> > Regards,
>> > Chitrak.
>>
>>
>