Re: Corrfunc output not generated

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 14 2016 - 17:41:44 CDT

Hello Sourav, the error is fixed:
https://github.com/colvars/colvars/commit/78dc9da14f7c19abdcf20fe24b59e1280e48284a

Please go to the README section of this webpage:
https://github.com/colvars/colvars
and follow the instructions about how to update the version of the colvars
module in your installation of NAMD.

Giacomo

On Tue, Apr 12, 2016 at 11:00 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hello Sourav, it looks like you are dealing with a different issue here
> from the post you linked. Recent versions of NAMD have introduced a
> different way of writing files, and the code that writes the correlation
> functions triggers an error. A message should have been printed.
>
> This error does not affect anything except the correlation function and
> other run-time analysis quantities.
>
> I'll send you a link to download a patch that fixes it.
>
> Giacomo
>
> On Tue, Apr 12, 2016 at 5:16 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hello Sourav, the issue was fixed. If you can reproduce the error with
>> NAMD 2.11, send me the configuration file and I'll test to see what's going
>> on.
>>
>> Giacomo
>>
>> On Mon, Apr 11, 2016 at 1:38 PM, Sourav Ray <souravray90_at_gmail.com>
>> wrote:
>>
>>> Greetings
>>>
>>> I tried to run corrfunc for the phi and psi angles from the NANMA
>>> exercise in the ABF tutorial section. Someone please tell me the error that
>>> might be preventing me from getting the output. I saw a relevant topic in
>>> the mailing list (
>>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/3695.html)
>>> but couldn't find whether it has been resolved in NAMD 2.10 that I have
>>> been using. The colvar input file is presented below:
>>>
>>> colvar {
>>> name phi
>>>
>>> dihedral {
>>> oneSiteSystemForce
>>> group1 {
>>> atomnumbers 13
>>> }
>>> group2 {
>>> atomnumbers 15
>>> }
>>> group3 {
>>> atomnumbers 17
>>> }
>>> group4 {
>>> atomnumbers 1
>>> }
>>> }
>>>
>>> corrfunc on
>>> corrfunctype coordinate
>>> corrFuncNormalize on
>>> corrfunclength 1000
>>> corrFuncStride 1
>>> corrFuncOffset 0
>>> corrFuncOutputFile phi.solv.corrfunc.dat
>>> }
>>>
>>> colvar {
>>> name psi
>>>
>>> dihedral {
>>> oneSiteSystemForce
>>> group1 {
>>> atomnumbers 3
>>> }
>>> group2 {
>>> atomnumbers 1
>>> }
>>> group3 {
>>> atomnumbers 17
>>> }
>>> group4 {
>>> atomnumbers 15
>>> }
>>> }
>>>
>>> corrfunc on
>>> corrfunctype coordinate
>>> corrFuncNormalize on
>>> corrfunclength 1000
>>> corrFuncStride 1
>>> corrFuncOffset 0
>>> corrFuncOutputFile psi.solv.corrfunc.dat
>>> }
>>>
>>> analysis on
>>>
>>> ////////////////////////////////
>>>
>>> Thanks and regards
>>> Sourav
>>>
>>
>>
>>
>> --
>> Giacomo Fiorin
>> Assistant Professor of Research
>> Institute for Computational Molecular Science (ICMS)
>> College of Science and Technology, Temple University
>> 1925 North 12th Street (035-07), Room 704D
>> Philadelphia, PA 19122-1801
>> Phone: +1-215-204-4213
>>
>> Scholar: http://goo.gl/Q3TBQU
>> Personal: http://giacomofiorin.github.io/
>> Lab page: https://icms.cst.temple.edu/members.html
>>
>> *"As computer programmers we have a responsibility to make sure that we
>> run the computers instead of the computers running us."* - Steve
>> Oualline
>>
>>
>>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
> *"As computer programmers we have a responsibility to make sure that we
> run the computers instead of the computers running us."* - Steve Oualline
>
>
>

-- 
Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
Scholar: http://goo.gl/Q3TBQU
Personal: http://giacomofiorin.github.io/
Lab page: https://icms.cst.temple.edu/members.html
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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