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

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sun May 27 2007 - 12:49:54 CDT

Indeed, very interesting. Thank you very much for the reply.

Cheers,

Michel

2007/5/27, Peter Freddolino <petefred_at_ks.uiuc.edu>:
> I think I'd rephrase that a bit less harshly. SHAKE (or, to be more
> accurate, rigidbonds, which usually uses SETTLE) brings benefits (in the
> form of a computational speedup) to all calculations, and is probably
> fine to use for most of them (as Himanshu pointed out, it's sort of the
> industry standard for MD these days). I'm suggesting a couple reasons
> that I (and other namd users) don't use it at the same levels as the
> rest of the MD community:
> -Although there's no clearly demonstrated example of this, the loss of
> coupling between high and low frequency modes of motion *could* give
> unphysical dynamics
> -There's a higher chance of innacuracies in some specific instances,
> such as when pressure profiles are important (hence the membrane issue)
> -It can be technically inconvenient in some circumstances, such as with
> systems >= 1 million atoms with constant pressure simulations
>
> What needs to be kept in mind here is that SHAKE is an approximation,
> just like MD itself is an approximation. When used appropriately it can
> be beneficial (in terms of simulation times), but if applied
> inappropriately it will lead to problems. As illustrated by the variety
> of successes in the larger MD community with using such techniques,
> *most* MD simulations are suitable for this approximation. A few cases
> (such as those highlighted above) may not be; also, unlike some other
> approximations, the potential time savings are not order of magnitude
> level, but rather on the order of 15-20%. I'm fairly certain that most
> of the MD community would view even this analysis as overly cautious,
> and it well may be. The best advice I can give is the same as what I did
> earlier: try some test runs on your simulation with and without
> rigidbonds if you have any doubts. For more run-of-the-mill simulations
> you may see people avoiding rigidbonds simply out of caution. To be
> frank, a lot of very smart people in MD use SHAKE for everything, and
> are probably correct to do so. I'd be very interested to see a good,
> in-depth analysis of the effects of SHAKE on some of the potential
> trouble cases, such as a large, long timescale membrane protein
> simulation; having not had the time to do this myself, nor seen it in
> the literature, I avoid rigidbonds in these cases. These should *not* be
> taken as hard rules; I'm just giving my $0.02.
>
> Peter
>
> L. Michel Espinoza-Fonseca wrote:
> > Very interesting. So basically you're suggesting (based on your own
> > experience) that SHAKE might bring some benefits when it comes to
> > simulate small systems (i.e., a peptide) for very long timescale
> > (i.e., more than 100 ns), but not when you simulate very big systems,
> > or those including a membrane. Could you add any additional rationale
> > for such selection?
> >
> > Cheers,
> >
> > Michel
> >
> > 2007/5/25, Peter Freddolino <petefred_at_ks.uiuc.edu>:
> >> 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.
> >> >>> -----------------------------------------------------
> >> >>>
> >> >>>
> >>
>

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