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

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 25 2007 - 09:52:47 CDT

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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