From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Sep 04 2012 - 04:31:05 CDT
Ipsita,
Please keep the list in CC so that others can follow this conversation.
The config file should not be changed for restarting (i.e. "centers
70" should stay that way), as NAMD should get from the restart file
information about the current stage of the transformation.
The very first stage should be numbered zero. Please look for output
lines mentioning changes in restraint centers in the log file of the
first NAMD run.
Finally, be aware that targetNumSteps gives the number of steps per
stage, not the total. The total simulation time should be
(targetNumStages + 1) * targetNumSteps.
The +1 is for sampling the last point: for 100 stages, there are 101
points to be sampled.
Sorry if the documentation was not explicit enough about this. We try
to improve it as we realize what's needed, thanks to user feedback
like yours.
Jerome
On 4 September 2012 10:10, ipsita basu <ibasu788_at_gmail.com> wrote:
> Thank you sir for your reply.
> Whatever I choose the value of centers, keeping fixed targetCenters
> 50.00 , the NAMD output is :
> colvars: Moving restraint stage 1 : setting centers to { 59.802 }.
> Then the center will move to 59.802 in the next 1000000 steps? Then
> what is the meaning of setting centers, and targetCenters?
> Yes I include the colvarsInput parameter as :
> colvarsInput out-us/da-us-1.out.res.colvars.state
>
> On 9/4/12, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>> Ipsita,
>>
>> Better than looking at the colvars trajectory, you can look in the
>> NAMD output for lines saying :
>> Moving restraint stage n : setting centers to x
>>
>> When restarting the job, do you add the colvarsInput parameter in the
>> NAMD config file?
>>
>> Cheers,
>> Jerome
>>
>>
>>
>> On 4 September 2012 07:42, ipsita basu <ibasu788_at_gmail.com> wrote:
>>> Sir,
>>> I have a query regarding restarting umbrella sampling simulation of
>>> membrane protein system.
>>> When I start it one portion of my configuration is:
>>> harmonic {
>>> name lenpot
>>> colvars distanceZ
>>> centers 70.00
>>> forceConstant 5.0
>>> targetCenters 60.00
>>> targetNumSteps 1000000
>>> targetNumStages 100
>>> where the distance between the two selected group is 70 which I want
>>> to decrease to 60 in 1000000 steps. The output traj is like:
>>> 999800 6.04585123909563e+01
>>> # step distanceZ
>>> 1000000 6.04704550193212e+01
>>> Now when I restart the job I set the above portion as :
>>> harmonic {
>>> name lenpot
>>> colvars distanceZ
>>> centers 60.00
>>> forceConstant 5.0
>>> targetCenters 50.00
>>> targetNumSteps 1000000
>>> targetNumStages 100
>>> But doing this the output traj file is like:
>>> 1403600 6.03582445087823e+01
>>> 1403800 6.03622946744465e+01
>>> which means the distance is not decreasing anymore, so I omit the
>>> option centers 60.00 and then I get the error: Error: must define the
>>> initial centers of the restraints.
>>> So should I set the value for centers and target centers, then what is
>>> the difference between the two?
>>> Or should I set off the options:
>>> targetCenters 50.00
>>> targetNumSteps 1000000
>>> targetNumStages 100
>>> Please help.
>>> --
>>> Ipsita Basu
>>> Research Fellow
>>> c/o : Dr. Chaitali Mukhopadhyay
>>> Rajabazar Science College
>>> 92 APC Road
>>> Kolkata - 700009
>>>
>>
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
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