[gmx-users] The pullf.xvg and pullx.xvg files

[Justin Lemkul]

On 6/26/15 10:34 AM, Laura Tociu wrote:
> Dear Justin,
>
> I have done two parallel short pullings, one with pull_geometry = cylinder
> and one with pull_geometry = direction.
>
> When pull_geometry = direction, everything works perfectly: the grompp
> output says that the distance at start, as well as the reference at t=0 are
> both equal to 3.019 nm, and the pullx.xvg file reflects this: at t=0 the
> distance is also 3.019 nm. This distance is reasonable based on my
> geometry. The force at t=0 is 10^-6 and the COM pull energy in the md.log
> file is on the order of 10^-10.
>
> When pull_geometry = cylinder, the grompp output says the distance at start
> and the reference distance are 1.215 nm (which they aren't) but the
> distance at t=0 in the pullx.xvg file shows up as 2.8 nm (which it is
> roughly -  it's hard to tell where the COM as computed by the cylinder
> approach would be but it is likely to be close to the COM as usually
> computed). This huge discrepancy leads to huge forces as well as energies
> at t=0.
>
> Is this some kind of bug that has been fixed since Gromacs 5.0.2, which is
> the version I'm using, or should I report it?  I think since the distance

Upgrading to 5.0.5 and trying again is the best way to answer that.  I don't 
know whether or not this is a bug.

> computed by grompp and that in the pullx.xvg file at t=0 are different, the
> method will likely give inaccurate forces and thus PMF's... What do you
> think?
>

Looking back over your setup again, I really don't think you need the cylinder 
geometry.  That's really intended for layers in which the reference atoms will 
change over time, as in the example shown in the manual.  Here, you have an ion 
and a protein; the reference atoms don't change, so some simpler geometry is 
more appropriate.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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