Re: Regular vs US sampling runs.

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Aug 31 2017 - 18:56:17 CDT

No. You probably have a colvar that is asking for waay too many atoms.
See
http://www.ks.uiuc.edu/Research/namd/2.12/ug/node56.html#SECTION000133400000000000000.
What does your colvar configuration file look like, and how many atoms
are being used in your reaction coordinate definition?

-Josh

On 08/31/2017 05:28 PM, jeevan gc wrote:
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> <div dir="ltr">Dear NAMD Users,
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> <div>I am running a Umbrella Sampling (US) Simulations using NAMD2.12 CUDA version &#43; a Quadro M5000 graphics card on 48 core linux machine. The all-atom membrane system has &nbsp;~32000 atoms.</div>
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> <div>The regular run takes 6 hours to complete &nbsp;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.</div>
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> <div>Is it normal for a US simulation time to be six times longer than a regular run?</div>
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> <div>Thank you in advance.</div>
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> <div>Jeevan</div>
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> <div>PS: &nbsp;&#43;16 CPU processors, saved at every 20ps, colvar frequency 10,000<br clear="all">
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> -- <br>
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> <div dir="ltr"><i><font face="times new roman, serif">Jeevan B. GC, Ph.D</font></i>
> <div><font face="times new roman, serif"><i>Post Doctoral Research Associate</i></font></div>
> <div><font face="times new roman, serif"><i>College of Pharmacy</i></font></div>
> <div><font face="times new roman, serif"><i>Washington State University</i></font></div>
> <div><font face="times new roman, serif"><i>Spokane, WA 99224 ,&nbsp;</i></font><i><font face="times new roman, serif">USA</font></i></div>
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