Regular vs US sampling runs.

From: jeevan gc (
Date: Thu Aug 31 2017 - 18:23:43 CDT

Dear NAMD Users,

I am running a Umbrella Sampling (US) Simulations using NAMD2.12 CUDA
version + a Quadro M5000 graphics card on 48 core linux machine. The
all-atom membrane system has ~32000 atoms.

The regular run takes 6 hours to complete 50ns. The same system in
umbrella sampling simulation takes 35 hrs to complete 50ns. The longer US
simulation time is due to additional harmonic restraint calculations.

Is it normal for a US simulation time to be six times longer than a regular

Thank you in advance.


PS: +16 CPU processors, saved at every 20ps, colvar frequency 10,000

*Jeevan B. GC, Ph.D*
*Post Doctoral Research Associate*
*College of Pharmacy*
*Washington State University*
*Spokane, WA 99224 , **USA*

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