From: ipsita basu (ibasu788_at_gmail.com)
Date: Tue Sep 04 2012 - 07:18:02 CDT
Thank you very much sir for your helpful reply. It is really needed.
Now I better understand the whole thing.
I'll need your help again for further progress.
Thank you again.
On 9/4/12, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> 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
>
-- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 700009
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