From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed May 02 2012 - 11:57:34 CDT
Please use 2.8 or later.
You're changing several options at the same time here (target centers,
pulling rate, etc): why not two different configuration files?
On Wed, May 2, 2012 at 12:54 PM, Wang Yi <dexterwy_at_gmail.com> wrote:
> 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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