Re: umbrella sampling

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Aug 22 2012 - 03:10:17 CDT

Ipsita,

The force constant is somewhat small, so you observe some amount of
fluctuation around the target value. Apart from that, everything seems
to be in order. That is, assuming that the collective variable
actually describes what you want to look at. Speaking of which, the
distanceZ function is described in the user's guide in plain English.
I can't add anything to that.

Best,
Jerome

On 22 August 2012 08:52, ipsita basu <ibasu788_at_gmail.com> wrote:
> Sir,
> I want to observe a protein penetration into membrane,that's why I
> want to do umbrella sampling simulation. The configuaration file where
> the umbrella sampling is enabled is given below:
> colvarsTrajFrequency 200
> colvar {
> width 1.0
> name distanceZ
> distance {
> group1 {
> atomNumbers 97280
> }
> group2 {
> atomNumbers 1235
> }
> }
> }
> harmonic {
> name lenpot
> colvars distanceZ
> centers 10.0
> forceConstant 1.0
> targetCenters -10.0
> targetNumSteps 2000000
> targetNumStages 30
> }
> where I put the value of z coordinate of 97280th atom in centers
> (centers 10.0). And I want to fix the process for the 97280th atom to
> reach from 10.0 to -10.0(targetCenters) in 2000000 steps.
> Am I doing right thing or not? Please help as the conception is not clear to me.
> And one more thing is that the traj file is look like:
> # step distanceZ
> 0 7.87607744204158e+01
> 200 7.31112828886414e+01
> 400 6.71194308765552e+01
> 600 6.29314331811324e+01
> 800 5.97378222403360e+01
> 1000 5.62958276760813e+01
>
> My question is that what is the meaning of distanceZ, is it the
> distance between the two selected atoms? Then by what rule it
> decreases, as the decrease is not same.
> Any type of suggestions will be really helpful to me. Please help.
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
>

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