From: yjcoshc_at_gmail.com
Date: Tue May 02 2017 - 04:15:21 CDT
Hello,
1. At this stage, you can use on-the-fly eABF to replace classical ABF
in any free-energy simulations, while egABF is also worth to try in high
dimensional free-energy calculations. On-the-fly eABF have three free
energy estimators: Naive, CZAR and zheng/yang's.
2. I am also puzzled with the total force change, but I have seen an
"subtractAppliedForce" option in the user guide. It can recover the
behavior before the change. If you have problems you can turn it on.
3. I don't know about it.
在 2017年04月29日 09:25, Jim 写道:
> Hello,
>
> I want to obtain free energy profiles of passages of molecules through
> nanopore systems immersed in an external electric field. I can use
> different free energy sampling schemes (cv-SMD/Jarzynski, (*)ABF, US,
> US-REMD, etc) to obtain PMFs. I have a couple questions related to
> that and to new NAMD releases:
>
> 1. Is there a method that is preferred (aiming at quantitative
> accuracy while possibly ignoring computational costs)?
>
> * a) For example, in regard to ABF, what can (and should) be used in
> the current NAMD version 2.12 (or CVS 2.13): ABF vs eABF vs
> on-the-fly eABF vs gABF vs egABF vs ...?
>
> I get confused between all these flavors and their applicability to
> the particular problem/system of interest.
>
>
> 2. Release notes of NAMD 2.12 in regard to Collective Variable Module:
>
> http://www.ks.uiuc.edu/Research/namd/2.12/features.html
>
> claim
>
> http://colvars.github.io/totalforce.html
>
> while a message from the mailing list from Mar 2015 reads:
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/0433.html
>
> This confuses me. If I want to go ahead with *new* ABF simulations
> under external electric field (that will affect *all* atoms in the
> simulation box regardless of CV), what should or should I not do to
> ensure accurate final results?
>
> 3. Again from the release notes:
>
> * "Scripting command "cvcflags" to optimize performance of complex
> colvars"
>
>
> I don't understand where and how the command "cvsflags" is and can be
> used. Is there an example usage?
>
> Thanks.
>
>
>
>
>
>
>
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