Re: Having problem with restarting colvar distance,

From: Aliasghar Alizadeh-Mojarad (ali.alizadehmoj_at_gmail.com)
Date: Wed Jan 03 2018 - 10:35:52 CST

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

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