Re: Regular vs US sampling runs.

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 31 2017 - 21:34:56 CDT

For 64 POPC molecules, you're talking about the center of mass of 3,300
atoms. Think about whether you can simplify that.

But in any case, centers of mass are computed in parallel (and used as such
by Colvars starting in NAMD 2.12) and a few thousand atoms shouldn't be too
much of a problem.

The Colvars output should tell you the size of each group of atoms. Can
you report those numbers?

Giacomo

On Thu, Aug 31, 2017 at 9:13 PM, jeevan gc <gcjeevanbdr_at_gmail.com> wrote:

> Thank you Josh for quick and very informative response.
>
> The system consists of a short helix and membrane (64 phospholipids). The
> reaction coordinate is defined as the center of mass between them. Both
> reference files are .pdb file with heavy atoms assigned occupancy of 1. I
> want to calculate the free energy of translocation across the bilayer.
>
> Thank you.
>
> Jeevan
>
> On Thu, Aug 31, 2017 at 4:56 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> wrote:
>
>> 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#SEC
>> TION000133400000000000000.
>> 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:
>> > <html>
>> > <head>
>> > <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
>> > </head>
>> > <body>
>> > <div dir="ltr">Dear NAMD Users,
>> > <div><br>
>> > </div>
>> > <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>
>> > <div><br>
>> > </div>
>> > <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>
>> > <div><br>
>> > </div>
>> > <div>Is it normal for a US simulation time to be six times longer than
>> a regular run?</div>
>> > <div><br>
>> > </div>
>> > <div>Thank you in advance.</div>
>> > <div><br>
>> > </div>
>> > <div>Jeevan</div>
>> > <div><br>
>> > </div>
>> > <div>PS: &nbsp;&#43;16 CPU processors, saved at every 20ps, colvar
>> frequency 10,000<br clear="all">
>> > <div><br>
>> > </div>
>> > -- <br>
>> > <div class="gmail_signature" data-smartmail="gmail_signature">
>> > <div dir="ltr">
>> > <div>
>> > <div dir="ltr">
>> > <div>
>> > <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>
>> > </div>
>> > </div>
>> > </div>
>> > </div>
>> > </div>
>> > </div>
>> > </div>
>> > </div>
>> > </body>
>> > </html>
>> >
>>
>>
>>
>
>
> --
> *Jeevan B. GC, Ph.D*
> *Post Doctoral Research Associate*
> *College of Pharmacy*
> *Washington State University*
> *Spokane, WA 99224 , **USA*
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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