|From:||Xinyi Shen <xinyis@...1683...>|
|Date:||Wed, 14 Jun 2017 12:51:17 +0000|
Dear Prof. Giacomo Fiorin,
Thank you! Your reply really helps a lot!
Have a great day!
发件人: Giacomo Fiorin [giacomo.fiorin@...24...]
发送时间: 2017年6月14日 6:54
收件人: Xinyi Shen
主题: Re: Questions about the output of Colvars and Multiple-replica metadynamics
Hi Xinyi, I'm copying the mailing list on my reply to share the information. Please do the same.
On Mon, Jun 12, 2017 at 9:32 PM, Xinyi Shen <xinyis@...1943....> wrote:
That depends on what you are using: metadynamics will write the 2D PMF automatically; ABF will need post-processing for anything above 1 dimension; umbrella sampling will also require post-processing.
How did you obtain the 2D PMF? If by metadynamics, try plotting it as a heat map or 3D surface. You should see a small region that is non-constant, but everything else is probably just not sampled yet.
That is only necessary when you have reached the strong scaling limit for a single replica but you still have compute nodes available, so you add more replicas for better statistics. Coupling the replicas (as opposed to averaging independent runs) is supposed to give you a quicker estimate of the optimal biasing potential to enhance the sampling.