From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 29 2021 - 06:30:58 CST
Hi Yogesh,
This is a question for the NAMD mailing list, I am cross-posting there.
The most important parameter here is probably fullSamples, which controls how soon the biasing force is applied when a free energy gradient is measured. If this happens much faster than other degrees of freedom can relax, the biasing force can be overestimated, and this will take a long time to relax, which can be monitored as the time it takes for the reverse transition to happen. So setting this parameter too low will increase the time to final convergence.
Best,
Jérôme
----- On 26 Nov 21, at 18:53, Yogesh Sharma <yogesh.rma13_at_gmail.com> wrote:
> Hi users
> I am trying to pull a ion through nanotubes. I was building on the NAMD
> tutorial. i divided my tube in 3 parts But the PMF in each part is increasing
> exponentially. considering force optimization i tried setting
> lower/upperwallconstants from 1, 5, 10, 100 but still results are similar--=_92cf137b-9fbb-4e70-b428-43c678c2a511--
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