VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Sep 25 2015 - 15:44:39 CDT

Also, I realized that we are never updating the *.top file after optimizing
the charges, which means that the *.top file has all atoms (except
aliphatic H) with 0.000 charge. Is that ok?

On Fri, Sep 25, 2015 at 4:43 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> Hi Christopher,
>
> Thanks for the explanation.
>
> I am trying to optimize the dihedrals. The current FFTK version shows
> "QME" and "MME" along with the fitting (so a total of 3). Could you tell me
> what the difference between these are? Also, the QME and MME are varying at
> some points. is that normal?
>
> I am attaching a pdf of my plot for your reference. Please note that it
> says "Orig" simply because I hit "Run Optimization" instead of "Run
> Refinement" during my last run by mistake. This is the result of a few
> rounds of optimization.
>
>
>
> Regards,
> Chitrak.
>
> On Wed, Sep 23, 2015 at 10:56 AM, Mayne, Christopher G <
> cmayne2_at_illinois.edu> wrote:
>
>> Chitrak,
>>
>> 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 Torsion Explorer is a new tool in VMD 1.9.3 alpha builds that is
>> designed to help map dihedral scans to the QM PES. At some point I was
>> parameterizing a troublesome molecule and was unable to get the dihedrals
>> to fit properly. It was difficult to identify which dihedral was causing
>> problems. The Torsion Explorer shows the plot of the QM PES (or whatever
>> scan log files are selected) and loads the scan trajectory into VMD. Each
>> scan is color coded in the PES; while moving through the trajectory, a
>> molecular representation identifying the dihedral that was scanned is shown
>> using the appropriate color coding. The Analyze Trajectory button computes
>> the current dihedral angle and the slope of the dihedral angle at every
>> scan point. This will allow you to see which dihedrals are changing the
>> most a particular part of the scan. Typically the dihedral that was being
>> scanned should be changing the most. In highly coupled systems, however,
>> this may not be the case, and it is often the source of problems when
>> trying to fit the overall PES.
>>
>> 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?
>>>
>>
>> The example molecule (pyrrolidine) in the screencasts contains
>> sp3-hybridized carbons. If you map the dihedrals between the atoms using
>> Newman projections, there are 3 local minima in the torsion (2 gauche and
>> one anti); this type of torsional profile is best represented with a
>> periodicity of 3.
>>
>> 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?
>>
>>
>> Multiplicity refers to the number of terms that are used to describe a
>> single dihedral. Periodicity is the number of minima in the torsion (n).
>>
>>
>> Regards,
>> Christopher Mayne
>>
>> On Sep 22, 2015, at 6:18 PM, Chitrak Gupta wrote:
>>
>> 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.
>>>>
>>>>
>>>
>>
>>
>