From: jiali wang (jialiwangnamd_at_gmail.com)
Date: Mon Jun 17 2019 - 09:20:41 CDT
Hi Jerome ,
Thank you for your reply. Trajectory is too big to send it. and just start
moment, the anion move to 28A far distance. I am using lasted version of
NAMD, and buildin with Colvars. I try to remove the outputApplied forced,
its still looks same, I am thinking about the "center" and "targetcenter"
function. from colvars.traj. it's looks like directly move to 28A distance.
I am still confused about it.
best,
Jiali
On Mon, Jun 17, 2019 at 5:23 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Hi Jiali,
>
> We need more information to understand this:
> 1) what version of Colvars are you using?
> 2) you need to remove the options you use that specifically disable
> valuable debug output:
> outputAppliedForce off
> outputCenters no
>
> And then the trajectory file will tell you exactly what is happening.
>
> Best,
> Jerome
>
>
> On Mon, 17 Jun 2019 at 03:21, Jiali Wang <jwang204_at_binghamton.edu> wrote:
>
>> HI everyone,
>> when I am setting colvar to sampling a ion passway, I expect to got a
>> continued passway, in 50000 steps. and then creating several windows based
>> on this coarse MD trajectory.
>> But somehow, the targetcenter is not working, could you please help me
>> with this? The simulation only recoginze "center" and use 26.8 as target
>> distance to apply harmonic force.
>>
>> Thank you!
>> jiali
>>
>> colvars writes as follow
>> harmonic {
>> name lenpot
>> colvars length
>> forceConstant 8 # in kcal/mol/A^2
>>
>> centers 26.8 # go from 25 Angstrom RMSD...
>> targetCenters 5.0 # ... to 1 Angstrom
>> targetNumSteps 500000 # in 500000 MD steps
>>
>> outputCenters no
>>
>>
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