Re: Regular vs US sampling runs.

From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Fri Sep 01 2017 - 11:32:27 CDT

Dr. Fiorin,

Thank you for your response.

There are 33 atoms in one group and 5888 atoms in another group.

I chose heavy atoms for the center of mass of the membrane. I am thinking
of selecting few atoms from each lipid such as P, N, O etc. in order to
reduce the number of atoms in group.

Thank you.

Jeevan

On Thu, Aug 31, 2017 at 7:34 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
> 

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

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