Re: Having problem with restarting colvar distance,

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Jan 03 2018 - 10:38:26 CST

Your problem is probably due to wrapping. See previous threads about it:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2106.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

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