Re: Having problem with restarting colvar distance,

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 03 2018 - 11:02:00 CST

Hi Ali, see also:
http://colvars.github.io/colvars-refman-namd/colvars-refman-
namd.html#sec:colvar_atom_groups_wrapping

and in particular the following warning:
Warning: enabling wrapAll can lead to inconsistent results for Colvars
calculations: please disable wrapAll, as is the default option in NAMD.
that is printed in all recent versions of the Colvars module, as the one
included in the NAMD version you are using.

In other words, Jérôme has pointed you already twice to a problem that you
would have been able to detect on your own by checking the log.

Please, always check the output for warnings.

Giacomo

On Wed, Jan 3, 2018 at 11:38 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Your problem is probably due to wrapping. See previous threads about it:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.201
> 4-2015/2106.html
>
> Best,
> Jerome
>
> ----- On Jan 3, 2018, at 5:35 PM, Aliasghar Alizadeh-Mojarad
> ali.alizadehmoj_at_gmail.com wrote:
>
> > Dear Jerome,
> > I would be pleased if you allow me to know it is my problem or it is kind
> > of bug which has been reported before since the nightly build of NAMD was
> > released.
> >
> > Best wishes,
> > Ali
> >
> > On Fri, Dec 29, 2017 at 1:46 PM, Aliasghar Alizadeh-Mojarad <
> > ali.alizadehmoj_at_gmail.com> wrote:
> >
> >> Dear Jerome,
> >> Thanks for your reply. I meant for all values, energies, pressure,
> colvar
> >> ... . Yes, I turned on the wrapAll. As I said NAMD works fine for the
> first
> >> run, but when I restart the run I get -nan for energies, ... .
> >>
> >> Best wishes,
> >> Ali
> >>
> >> On Fri, Dec 29, 2017 at 3:34 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> >> wrote:
> >>
> >>> Hi Ali,
> >>>
> >>> Where do you see NaN values: as energies? Colvar values? Does this
> happen
> >>> at the very first timestep? Did you enable the wrapAll keyword?
> >>>
> >>> Jerome
> >>>
> >>> On 29 December 2017 at 09:10, Aliasghar Alizadeh-Mojarad <
> >>> ali.alizadehmoj_at_gmail.com> wrote:
> >>>
> >>>> Dear All,
> >>>> I encountered an error when restarting my simulation including
> >>>> restraining the COM of group of atoms by using colvar. NAMD works
> fine with
> >>>> colvar but when I restart the run I get a bunch of -nan -nan which I
> see if
> >>>> my simulation is bogus. I have the following lines in my NAMD conf
> file to
> >>>> restart the colvar.
> >>>> ====
> >>>>
> >>>> colvars on
> >>>> incr RunNo -1
> >>>> colvarsConfig $colvinp
> >>>> colvarsInput r${RunNo}.colvars.state
> >>>> ====
> >>>> The colvinp is :
> >>>> ===
> >>>> colvarsTrajFrequency 100
> >>>> colvarsTrajAppend off
> >>>> analysis off
> >>>> colvar {
> >>>> name system
> >>>> distance {
> >>>> group1 {
> >>>> atomsFile constrain-colvar.pdb
> >>>>
> >>>> atomsCol B
> >>>> atomsColValue 1.0
> >>>> }
> >>>> group2 {
> >>>> dummyAtom (0, 0, 0)
> >>>> }
> >>>> }
> >>>> }
> >>>> harmonic {
> >>>> colvars system
> >>>> centers 0.0
> >>>> forceConstant 2.0
> >>>> }
> >>>> ========
> >>>>
> >>>> I found a kind of similar error which was reported last year. I am
> >>>> using the last version of NAMD which is super fast. I would be
> pleased if
> >>>> anybody can help me to find out what is the problem.
> >>>>
> >>>> Best wishes,
> >>>> Ali
> >>>> --
> >>>> Sincerely,
> >>>> Aliasghar Alizadeh-Mojarad
> >>>>
> >>>>
> >>>
> >>
> >>
> >> --
> >> Sincerely,
> >> Aliasghar Alizadeh-Mojarad
> >>
> >>
> >
> >
> > --
> > Sincerely,
> > Aliasghar Alizadeh-Mojarad
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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