Re: Having problem with restarting colvar distance,

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Dec 29 2017 - 04:34:56 CST

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
>
>

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