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

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Fri May 25 2007 - 10:07:55 CDT

Peter,

Thank you very much for the insights,

----------------------------
Himanshu Khandelia, PhD
WWW: www.memphys.sdu.dk/~hkhandel
-----------------------------

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 Célia Araújo 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.
> >>> -----------------------------------------------------
> >>>
> >>>
>

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