Re: ABF - coordNum collective variable

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Mar 19 2012 - 10:47:45 CDT

Hi Adam,

You can still run ABF by enabling the extendedLagrangian option - this
is still a little experimental but should work well. This combination
may be called eABF, for "extended-system ABF". It will be properly
documented soon.

For best results, set extendedFluctuation to something small (e.g.
close to the bin width) and extendedTimeConstant to 200 fs.

Best,
Jerome

On 16 March 2012 16:59, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
> Hello Adam, the coordNum component does not have all the derivatives
> implemented that are necessary to do ABF.  If you absolutely need to
> use it to compute a free energy, Jérôme can give you suggestions on
> how to adapt it to ABF, or you can also try metadynamics.
>
> Bests
> Giacomo
>
> On Thu, Mar 15, 2012 at 4:27 PM, Adam Skelton <mradamskelton_at_hotmail.com> wrote:
>> Dear NAMD developers/experts,
>>
>> I was just wondering if the coordnum collective variable works at the moment
>> (with ABF).
>>
>> I get this error message when I tried to use it in the same way I would with
>> a distance collective variable.
>>
>> colvars:   Error: one or more of the components of colvar "COMDistance" does
>> not support system force calculation.
>> colvars:   If this error message is unclear, try recompiling with
>> -DCOLVARS_DEBUG.
>> FATAL ERROR: Error in the collective variables module: exiting.
>>
>> here is my input file
>>
>> colvar {
>>   name COMDistance
>> outputSystemForce no
>> lowerboundary  0
>>   upperboundary  10
>>
>>   lowerwallconstant 100
>>   upperwallconstant 100
>>
>>
>> coordNum {
>> group1  {
>> atomnumbers {44128 44129}
>> }
>> group2 {
>> atomsFile             mid1.pdb
>>  atomsCol              B
>>  atomsColValue         1
>> disableForces
>> }
>>
>> }
>> }
>>
>>
>> abf {
>> colvars COMDistance
>> fullSamples 50
>> }
>>
>> I am using the windows executable (NAMD_2.8_Win32-multicore), downloaded
>> yesterday, but have run into similar problems with different versions too.
>>
>> I would appreciate any help, this would be a very useful collective variable
>> for me!
>>
>> Thank you in Advance
>>
>> Adam
>>
>>
>

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