From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 12 2016 - 22:00:04 CDT
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
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