From: Aliasghar Alizadeh-Mojarad (ali.alizadehmoj_at_gmail.com)
Date: Fri Dec 29 2017 - 14:46:29 CST
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
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