Re: Having problem with restarting colvar distance,

From: Aliasghar Alizadeh-Mojarad (ali.alizadehmoj_at_gmail.com)
Date: Wed Jan 03 2018 - 13:44:19 CST

Dear Jerome and Giacomo,
Thank you very much for your replies.
I think I could solve my problem based on what you and Jerome pointed out.
I always do so and that warning has already concerned me.
Thanks again.

Best wishes,
Ali

On Wed, Jan 3, 2018 at 10:02 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
>

-- 
Sincerely,
Aliasghar Alizadeh-Mojarad

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