[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations?

[unitALX]

Yar, I understand. However, because of the differences in software
experience (NAMD / GROMACS), presenting literature references is not as
effective as I thought it would be, historical inertia and spirited
argumentation is having more weight than I thought it would, and in between
what is published for GROMACS and his best practice methods for NAMD, there
is a gray area for which is effectively being biased towards NAMD style
protocols (or what have you) and while you are correct in the long-term
thermodynamic limit of publishing work, I have kinetic barrier to overcome
in explaining something to someone who has seniority over me in my place of
work and whose advice gives the de facto direction of the work I do. Hence
why I am asking this more gray question of how to "justify" and "explain"
across the software divide what I think are faster but valid choices for
protocols. It is with considerable uneasiness that I see explanations being
made in this gray area that are not consistent with the papers I am
reading.

To be more blunt about my situation, we are in a gray area on the choice of
a homology model whose stability is being assessed by dynamics, and I am
hearing people say things like "well its a gray area, we can just argue it
this way, or that way, and then we'll submit the results to a journal, and
if they don't agree, we'll just submit the same work to another journal". I
face a higher burden of proof than the textbook approach. Please advise.


On Tue, Feb 11, 2014 at 4:12 PM, TomPiggot [via GROMACS] <
ml-node+s5086n5014470h92 at n6.nabble.com> wrote:

> Hi,
>
> Personally I would also ask your colleague if he could also provide
> evidence (e.g. published papers) to back up what he is saying to you (i.e.
> that it is necessary to use a 1 fs timestep with an NVE ensemble to achieve
> acceptable results). This way, you can make an informed decision based upon
> the available evidence you can find, rather than simply upon one persons
> view point. I would suggest the he will find it difficult to come up with
> such evidence for your case of a straight forward MD simulation.
>
> You should also remember that you are the one that will need to be able to
> defend (to an examiner or reviewer) what you have done and why. Simply
> "because the postdoc told me it was the correct thing to do" will
> (unfortunately) not be good enough!
>
> Cheers
>
> Tom
> ________________________________________
> From: [hidden email]<http://user/SendEmail.jtp?type=node&node=5014470&i=0>[[hidden
> email] <http://user/SendEmail.jtp?type=node&node=5014470&i=1>] on behalf
> of Szilárd Páll [[hidden email]<http://user/SendEmail.jtp?type=node&node=5014470&i=2>]
>
> Sent: 11 February 2014 13:33
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] "Justifying" 4fs production runs after 1fs
> equilibrations?
>
> On Tue, Feb 11, 2014 at 12:11 PM, unitALX <[hidden email]<http://user/SendEmail.jtp?type=node&node=5014470&i=3>>
> wrote:
>
> > Helllo all!
> >
> > In my general situation, I have a batch of homology models that I would
> like
> > to assess for stability by molecular dynamics.
> >
> > I am working with a postdoc in my lab who was extensive experience with
> > NAMD, but does not use GROMACS. We have been developing protocol for
> these
> > MD simulations, but we had some different views on equilibration and
> > production.
> >
> > Equlibration
> > My friend is recommending that I do equilibration for 500ps @ 1fs with
> no
> > constraints. I have no real objection to that, but he made it seem like
> the
> > results might be quite different than an equilibration for 200ps @ 2fs
> with
> > LINCS all-bonds. Would it make a critical difference?
> >
> > Production
> > I was excited by the performance possible with LINCS all-bonds, -vsite
> > aromatics @ 4fs, but my friend looks at 4fs with disgust.
>
> I would you mind asking your friend whether multiple time stepping
> disgusts him too? :)
>
> --
> Szilárd
>
> > I responded with
> > arguments from the GROMACS 4 paper, and a paper called "Improving
> efficiency
> > of large time-scale molecular dynamics simulations of hydrogen-rich
> systems"
> > re: the relationship between the period of the fastest vibration and
> largest
> > allowable timestep, but he seems quite convinced that for publication,
> only
> > 1fs and possibly 2fs production runs (preferably without barostat and
> > thermostat??) are acceptable. The suggestion to drop the barostat and
> > thermostat for production follows the philosophy that if your
> minimization
> > and equilibration is properly done, then the system should be stable in
> > production without pressure & temperature control. I'm having a hard
> time
> > finding better literature "justifications" for usage of LINCS all-bonds
> @
> > 2fs, and certainly for -vsites @ 4fs; P&T control seems quite standard
> in
> > publications using GROMACS.  Can you suggest any papers or calculations
> I
> > can do to show the validity of these options?
> >
> > --
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