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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