[gmx-users] A questin to Justin on methods in the PPARγ-RXRα-DNA complex paper

Justin Lemkul jalemkul at vt.edu
Sat Feb 20 20:18:22 CET 2016

On 2/20/16 1:59 AM, Timofey Tyugashev wrote:
> I was looking for examples of calculation setups. So I have a couple of
> questions about one used in this paper
> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008
> Parameters are amber99sb-ildn and gaff:
> "Simulations were carried out with GROMACS [40,41], version 4.6. All bonds were
> con-
> strained using the P-LINCS algorithm [42], allowing an integration time step of
> 2 fs. The Verlet
> cutoff scheme [43] was used with a minimum cutoff of 1.0 nm for short-range
> Lennard-Jones
> interactions and the real-space contribution to the smooth Particle Mesh Ewald
> algorithm
> [44,45]"

If you have questions about any of my papers, it's generally preferred to send 
them directly to me, rather than airing them out over the mailing list.

> Why all-bonds constraints are applied? Isn't AMBER FF are supposed to be used
> with h-bond constraints? Is there any notable difference between 1 and 2fs
> timestep in this setup?

Any difference between constraining all bonds and h-bonds is probably 
negligible.  As has been noted several times on the list in response to your 
questions, there are implementation differences and other assumptions that are 
often very different between programs.  Different nonbonded schemes, constraint 
algorithms (LINCS vs. SHAKE), etc. make for a lot of potential differences that 
have rather unknowable consequences.

I don't really know how to answer the second question.  There's no point wasting 
time at 1 fs when the simulation can stably be simulated with dt = 2 fs, 
especially for something this large.

> Is box-solute distance of 1.0nm sufficient for 1.0nm LJ cuttof?

This was already answered the other day.  A box-solute distance of 1.0 nm leaves 
2.0 nm between solute images.  It's enough.

> And why run three independent 500ns simulations instead of one or two of longer
> duration? Only to check for reproducibility or are there any additional reasons?

Mostly for better sampling.  All simulations behave somewhat differently, but 
generally you can observe the same average behavior.  A single, long simulation 
may get stuck in a minimum and give the false impression of convergence. 
Multiple simulations that converge to compatible behavior is more credible.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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