Hi Dave,
This can be done with PLUMED. I have recently seen that the Amber development version has a working interface for pmemd.
I have used PLUMED with sander before to compute the PMF for pulling n2o5 out of a liquid water slab (see
https://dx.doi.org/10.1039/c8cp03022g). Below is the PLUMED input for putting umbrella potentials at <DIST> along the z-component of the COM distance between two groups of atoms:
UNITS LENGTH=A ENERGY=kcal/mol TIME=fs
nox: COM ATOMS=1-7 NOPBC
wat: COM ATOMS=8-4103 NOPBC
d3: DISTANCE ATOMS=wat,nox COMPONENTS
RESTRAINT ARG=d3.z AT=<DIST> KAPPA=5.0
PRINT STRIDE=1 ARG=d3.z FILE=COLVAR
ENDPLUMED
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Jan 18, 2020, at 5:14 AM, David Case <david.case.rutgers.edu> wrote:
>
> Is there a built-in way in pmemd to define a progress variable (aka
> reaction coordinate) for umbrella sampling to be the z-component of the
> center-of-mass of some group of atoms?
>
> We have a lipid bilayer with the normal along the z-axis, and would like
> to estimate a PMF for pulling a peptide out of the membrane.
> Suggestions for other/better ways to do this are also welcome.
>
> ....thx...dac
>
>
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Received on Sat Jan 18 2020 - 18:30:01 PST
