Re: Regular vs US sampling runs.

From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Fri Sep 01 2017 - 16:32:20 CDT

Thank you Josh.

I use NAMD 2.12. The system is re-centred before performing umbrella
sampling runs. I will reduce the number of atoms by selecting atoms in the
middle of the membrane and will update the simulation time. I hope this
will not compromise my results with previous results.

Thank you.

Jeevan

On Fri, Sep 1, 2017 at 9:53 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> You wouldn't happen to be using NAMD 2.11, would you? In that case, it
> would indeed be very slow. What I did for a similar kind of calculation was
> indeed to only use a selected number of atoms to compute the center of
> mass. However, since the COM calculation handles motion of lipids across
> the periodic image a bit less gracefully than might be desired, I would
> advocate for recentering your system so that the center of the bilayer is
> aligned to the center of the periodic cell before you start, and maybe
> using the atoms in the middle of your membrane to define the center.
>
> As another word of warning: the z-position may not be the right reaction
> coordinate if you are interested in membrane binding. For larger molecules
> interacting with the membrane, the different potential orientations with
> respect to the membrane could get you radically different interactions, and
> as a result your convergence would be super slow (see 10.1021/jp501622d) as
> it needs to sample along an orthogonal degree of freedom that you aren't
> biasing. What I did when looking at membrane attachment was to use
> something like a contact number instead (coordnum in colvars,
> 10.1021/acs.biochem.6b00468), which has a much easier time converging.
>
> -Josh
>
> On 09/01/2017 10:32 AM, jeevan gc wrote:
> 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<
> mailto: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<mailto:
> 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<
> mailto: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#
> SECTION000133400000000000000<https://na01.safelinks.
> protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%
> 2FResearch%2Fnamd%2F2.12%2Fug%2Fnode56.html%23SECTION000133400000000000000
> &data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cff909d95dfb64c29e11908d4f157
> 09b9%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%
> 7C636398803510087946&sdata=wr62RHteTXWfKBLLmoekhUKjQHLplb
> P95y83h%2F9HJgw%3D&reserved=0>.
> 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.
> outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%
> 7C01%7CJoshua.Vermaas%40nrel.gov%7Cff909d95dfb64c29e11908d4f15709b9%
> 7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636398803510087946&sdata=
> wmEvpbYssl2XST3gEGIhVjEqAkFJzLMxTdJ3JlxVtlA%3D&reserved=0>
>
https://github.com/giacomofiorin.
> safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.
> com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%
> 7Cff909d95dfb64c29e11908d4f15709b9%7Ca0f29d7e28cd4f5484427885aee7
> c080%7C0%7C0%7C636398803510087946&sdata=UInhjwhkeTQEKdQUEfTpLJnI4nIE0m
> %2F2MD6MDc2Mapg%3D&reserved=0>
>
>
>
> --
> Jeevan B. GC, Ph.D
> Post Doctoral Research Associate
> College of Pharmacy
> Washington State University
> Spokane, WA 99224 , USA
>
>

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

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:37 CST