From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Sep 04 2012 - 02:48:15 CDT
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
>
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