Hi! I don't know if it is what you are looking for, but in page 537 of
Amber reference manual it says:
fxyz
If iat(3)=0 and igr1 and/or igr2 is defined then it is possible to weight
the x, y, z components of
the force in the restraint to 0 (no force) or 1 (full restraint force). Ex:
fxyz=0, 0, 1. This sets
no additional restraint force on the x component or y-component of the
restraint force, and full z-
component restraint force. Default fxyz=1,1,1. Note: When setting fxyz, the
r1, r2, r3, r4 values
should be set relative to a weighted distance q
(wx ∗ dx)
2 + (wy ∗ dy)
2 + (wz ∗ dz)
2
, so if fxyz=0,0,1
then the only distance taken into account when comparing to r1,r2,r3,r4 is
the z distance between
the molecule and the center of mass. Note that the DUMPAVE value when
outxyz=0 is also just the
weighted distance.
Hope it helps!
Gera!
El sáb., 18 de ene. de 2020 23:02, Goetz, Andreas <agoetz.sdsc.edu>
escribió:
> 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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>
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Received on Sat Jan 18 2020 - 18:30:02 PST
