Re: Why is SHAKE not being used in typical NAMD simulations ?

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sat May 26 2007 - 01:03:25 CDT

Oops, I missed the parameter nonbondedfreq=2, sorry. ok, that is what
probably causes the speed up. Has anyone performed extensive benchmarks
with/without SHAKE and with/without multistep and posted them online?

Now I'm performing a benchmark with a 1/2/4 time step. Let's see what the
outcome will be.

Gianluca

On Fri, 25 May 2007, Gianluca Interlandi wrote:

> Hello Peter,
>
> You say only 15% speedup? I have just performed a benchmark on 32 CPUs of
> NCSA SGI Altix. My system contains 96106 atoms. If I run it with a 2 fs
> timestep and SHAKE it takes 3796.5 sec to perform 100 psec (i.e. 50'000
> steps). If I turn off SHAKE and use a 1 fs timestep it takes 7382.5 sec to
> perform 100 psec (i.e. 100'000 steps). Thus I do get a speedup of 94%
> thanks to SHAKE and 2 fs timestep. What do I do differently than other
> people who get only 15-25%?
>
> Some simulation details: in both benchmarks I used PME, langevin
> temperature and pressure control, switchdist=10.0, cutoff=12.0,
> pairlistdist=14.0, stepspercycle=10, fullElecFreq=1 (default). I did not
> use a multistep (fullElecFreq=4) when SHAKE was off but I don't think that
> this would make such a large difference.
>
> Or, does the scalability of SHAKE break down only with very large systems
> and a very large number of CPUs?
>
> Another question: you say that you don't use SHAKE for very large
> simulations. Can you please give an example of what very large could be?
>
> I apologize if I'm creating confusion. I use SHAKE a lot and thus I want
> to better understand its pro/contra.
>
> Many thanks,
>
> Gianluca
>
> On Fri, 25 May 2007, Peter Freddolino wrote:
>
> > Hi Himanshu,
> >
> > I think there are several reasons for this; some might be considered
> > "good" and some not. First, I'd like to clarify something. A bit earlier
> > you said
> >
> > I am hoping some of the developers will
> > be able to tell us why SHAKE is not recommended in NAMD, while it is in
> > other programs?
> >
> >
> > The issue is not that SHAKE is not recommended in NAMD; it is just as
> > advisable in NAMD as in any of the other common MD programs. Please
> > note, also, that the NAMD "developers" and "users" are mostly disjoint
> > sets; it isn't the developers deciding not to use SHAKE, but the users.
> > The issue is just that people in that people in the NAMD community (and,
> > in particular, the KS group) tend to be those that avoid using SHAKE for
> > most applications. This is in large part due to lingering concerns about
> > coupling of different frequency modes of motion (as pointed out by Ana)
> > and pressure profile calculations (see, e.g., JCC 121:8611); this
> > concern is particularly acute within the NAMD community because people
> > tend to do large simulations, frequently containing membranes, and have
> > not yet been adequately convinced that for these applications no
> > pathologies with SHAKE will occur to make it worthwhile using SHAKE for
> > a 15% speedup. SHAKE convergence can also be problematic when using very
> > large systems in constant pressure simulations, which (again) is fairly
> > common in the NAMD community. The speedup from SHAKE also gets less
> > impressive as more processors are used.
> >
> > Some part of this difference is also due to institutional memory; I have
> > no doubt that there are a lot of simulations done without rigid bonds
> > even where they would be fine, because of the concerns highlighted
> > above, and the fact that people in the NAMD community tend to put more
> > stock in those concerns (even in cases where they may not be valid) and
> > choose to err on the side of caution. I know for my own research, I'm
> > using SHAKE in some simulations (particularly those involving long
> > timescale exploration of relatively small systems) but not others (those
> > where I have a membrane or other concerns about the pressure, or very
> > large simulations).
> >
> > You're absolutely correct that SHAKE is quite widely used in
> > biomolecular simulations, and is well tested for most of these
> > applications. Whether or not SHAKE should be applied to any given
> > simulation comes down to personal preference, and an evaluation of
> > whether or not the specific places where it *could* in principle cause
> > trouble are important to your case (preferably including some short
> > simulations of your system with and without SHAKE). I know that people
> > around here are starting to test and use SHAKE a bit more; I think the
> > main reason it isn't used more widely is that the speed improvements
> > aren't, say, on the order of 2x, and for a lot of systems SHAKE doesn't
> > seem worth the risk (that some artifact might appear) or hassle (of
> > running a comparison simulation). Please note that I'm not being
> > cavalier about computing time: a 15% speedup seems much less worthwhile
> > if it costs you 10% more simulation (without rigidbonds, for comparison
> > purposes) or 100% of your simulation (if some sort of problem occurs).
> >
> > Peter
> >
> > Himanshu Khandelia wrote:
> > > It is not entirely true that people shy away from SHAKE. All typical
> > > biomolecular MD simulations use SHAKE very widely, except those
> > > implemented in NAMD. So people do shy away from SHAKE, but only when using
> > > NAMD.
> > >
> > > ----------------------------
> > > Himanshu Khandelia, PhD
> > > Research Assistant Professor (Postdoc)
> > > MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
> > > University of Southern Denmark (SDU)
> > > Odense M 5230, Denmark
> > >
> > > Phone: +4565503510
> > > email: hkhandel_at_memphys.sdu.dk
> > > WWW: www.memphys.sdu.dk/~hkhandel
> > > -----------------------------
> > >
> > >
> > >
> > > On Thu, 24 May 2007, Ana Celia Araujo Vila Verde wrote:
> > >
> > >
> > >> Here's my two cents about this issue,
> > >>
> > >> There's a physical reason why people shy away from SHAKE, in particular
> > >> when very interested in getting accurate dynamics: slow and fast
> > >> vibrational modes "talk" to each other, and fast modes may influence
> > >> slow modes. See Baysal, C., et al., Molecular dynamics analysis of
> > >> coupling between librational motions and isomeric jumps in chain
> > >> molecules. Macromolecules, 1996. 29(7): p. 2510-2514.
> > >>
> > >> Getting rid of fast modes by using SHAKE can thus have unexpected
> > >> outcomes in a simulation. So, I'd be comfortable using SHAKE for
> > >> Equilibration in most situations, but I'd evaluate carefully whether the
> > >> 15-20% gains in simulation time are worth the extra uncertainty for
> > >> actual runs. Normally, whether I use SHAKE or not depends on the
> > >> problem I'm studying. If I do use SHAKE, I normally run a comparison
> > >> simulation without it and compare the results to make sure no
> > >> significant differences occur. Most of the time, however, I find the
> > >> extra hassle of running that comparison simulation to be a big pain and
> > >> not worth it for a 15% gain, so I just don't use SHAKE...
> > >>
> > >> I hope this helps,
> > >>
> > >> Ana
> > >>
> > >>
> > >>
> > >> _________________________________
> > >> Ana CÚlia Ara˙jo Vila Verde
> > >> Penn State University
> > >> Department of Chemical Engineering
> > >> Fenske Laboratory
> > >> University Park, PA 16802
> > >> USA
> > >>
> > >>
> > >> Phone: +(1) (814) 863-2879
> > >> Fax: +(1) (814) 865-7846
> > >> avilaverde_at_engr.psu.edu
> > >> http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
> > >> http://www.gfct.fisica.uminho.pt/Members/acvv
> > >> _________________________________
> > >>
> > >>
> > >>
> > >> -----Original Message-----
> > >> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Himanshu Khandelia
> > >> Sent: Thursday, May 24, 2007 9:47 AM
> > >> To: Gianluca Interlandi
> > >> Cc: namd-l_at_ks.uiuc.edu
> > >> Subject: Re: namd-l: Why is SHAKE not being used in typical NAMD simulations ?
> > >>
> > >>
> > >> Please note that this post is not about using multiple time stepping, and
> > >> energy drifts. It is about SHAKE. I am hoping some of the developers will
> > >> be able to tell us why SHAKE is not recommended in NAMD, while it is in
> > >> other programs ?
> > >>
> > >> ----------------------------
> > >> Himanshu Khandelia, PhD
> > >> Research Assistant Professor (Postdoc)
> > >> MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk University of Southern Denmark (SDU) Odense M 5230, Denmark
> > >>
> > >> Phone: +4565503510
> > >> email: hkhandel_at_memphys.sdu.dk
> > >> WWW: www.memphys.sdu.dk/~hkhandel
> > >> -----------------------------
> > >>
> > >>
> > >>
> > >> On Wed, 23 May 2007, Gianluca Interlandi wrote:
> > >>
> > >>
> > >>> There have been already discussions in the NAMD list about the use of
> > >>> different timesteps. In particular, it seems that the use of a multi
> > >>> stepping algorithm seems to cause an energy drift:
> > >>>
> > >>> http://www.ks.uiuc.edu/~sotomayo/private/answer.html
> > >>>
> > >>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5385.html
> > >>>
> > >>> Usually, the conservation of energy is used as a "quality control" for
> > >>> the
> > >>> algorithm and timestep used. Thus if you are concerned about whether the
> > >>> chosen timestep is good or not the first thing to do would be to check
> > >>> whether the energy and temperature are conserved.
> > >>>
> > >>> Gianluca
> > >>>
> > >>> On Wed, 23 May 2007, L. Michel Espinoza-Fonseca wrote:
> > >>>
> > >>>
> > >>>> Note: I mentioned this thing about being reliable enough because
> > >>>> others have told me that, so I just said what I was told by my
> > >>>> colleagues, and it doesn't represent my own view :).
> > >>>>
> > >>>> 2007/5/23, Eric Cyr <ericcyr_at_uiuc.edu>:
> > >>>>
> > >>>>> What is meant by "not reliable enough"? I can think of a couple of
> > >>>>> things this could mean.
> > >>>>>
> > >>>>> Eric
> > >>>>>
> > >>>>> On 5/23/07, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
> > >>>>> wrote:
> > >>>>>
> > >>>>>> I myself have asked this question before. My answer (as before)
> > >>>>>> is no idea. Perhaps some people think that SHAKE and MTS schemes
> > >>>>>> are not reliable enough (at least this is what some colleagues
> > >>>>>> have told me before).
> > >>>>>>
> > >>>>>> Cheers,
> > >>>>>> Michel
> > >>>>>>
> > >>>>>> 2007/5/23, Himanshu Khandelia <hkhandel_at_memphys.sdu.dk>:
> > >>>>>>
> > >>>>>>> Hello,
> > >>>>>>>
> > >>>>>>> Most NAMD papers describe a simulation timestep of 1 fs, no
> > >>>>>>> shake, a nonbondedfreq of 2, and an fullelecfreq. of 4. This
> > >>>>>>> is also what is recommended in most NAMD tutorials.
> > >>>>>>>
> > >>>>>>> However, use of a 2 fs timestep, a value of 1 for both the
> > >>>>>>> nonbondedfreq and fullelecfreq results in 15-25 % faster
> > >>>>>>> performance in my tests. I can provide more details of the
> > >>>>>>> tests if desired, but surely these tests must
> > >>>>>>> have already been performed.
> > >>>>>>>
> > >>>>>>> So why is SHAKE/RATTLE and a larger time step not being used
> > >>>>>>> for most simulations?
> > >>>>>>>
> > >>>>>>> Thank you for the help,
> > >>>>>>>
> > >>>>>>> -Himanshu
> > >>>>>>>
> > >>>>>>> ----------------------------
> > >>>>>>> Himanshu Khandelia, PhD
> > >>>>>>> Research Assistant Professor (Postdoc)
> > >>>>>>> MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
> > >>>>>>> University of Southern Denmark (SDU) Odense M 5230, Denmark
> > >>>>>>>
> > >>>>>>> Phone: +4565503510
> > >>>>>>> email: hkhandel_at_memphys.sdu.dk
> > >>>>>>> WWW: www.memphys.sdu.dk/~hkhandel
> > >>>>>>> -----------------------------
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>> --
> > >>>>> 4330 Siebel Center
> > >>>>> 201 N. Goodwin Ave.
> > >>>>> Urbana, IL 61801
> > >>>>> http://www.cse.uiuc.edu/~ericcyr/
> > >>>>>
> > >>>>>
> > >>> -----------------------------------------------------
> > >>> Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> > >>> +1 (206) 685 4435
> > >>> +1 (206) 714 4303
> > >>> http://biocroma.unizh.ch/gianluca/
> > >>>
> > >>> Postdoc at the Department of Bioengineering
> > >>> at the University of Washington, Seattle WA U.S.A.
> > >>> -----------------------------------------------------
> > >>>
> > >>>
> >
>
> -----------------------------------------------------
> Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://biocroma.unizh.ch/gianluca/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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