Re: Question about targetsNumSteps in ColVar

From: Wang Yi (dexterwy_at_gmail.com)
Date: Wed May 02 2012 - 11:54:20 CDT

Thanks Giacomo!

Yeah I looked at the user guide for NAMD2.7b1 (that's saved in my bookmark). My bad.

Basically what I'm trying to do is to do SMD with two pulling rate, a fast pulling from 0 to 4.0 A, and a slow pulling from 4.0 to 13.0. Is there any way to implement this in one colvar? Thanks.

Best,
___________________________

Yi (Yves) Wang
Duke University

On 2012-5-2, at 下午12:38, Giacomo Fiorin wrote:

> Hello Yi, first of all, "targets" is not a keyword as you will notice from quickly browsing the user's guide. "targetCenters" is, and it gets the centers for multiple colvars, not different centers for the same colvar.
>
> If you want to do consecutive runs, you can use targetNumStages, to do several intermediate discrete steps between where your centers are and where your targets are. But all of your stages have to have the same targetNumSteps, which is going to be only one number (either 40000 or 90000).
>
> Everything is explained in more detail here (3rd result after you Google some of the keywords you mentioned):
>
> http://www.ks.uiuc.edu/Research/namd/2.7/ug/node50.html#SECTION000123700000000000000
>
> On Wed, May 2, 2012 at 9:52 AM, Wang Yi <dexterwy_at_gmail.com> wrote:
> Hi NAMDers,
>
> I have one confusion about using multiple targets in the harmonic block of ColVar. It's probably been answered before, but I can't find related messages through google.
>
> Say I set two targets at "targets 4.0 13.0" and I want the first target to be reached in 40000 steps, and the second to be reached in 90000 steps. The total number of steps will be 130000 steps.
> For the "targetsNumSteps" entry, should I put "40000 90000" or "40000 130000"?
>
> Thanks and best regards,
>
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
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