[gmx-developers] programming gromacs -> WHAM ?

Michael Brunsteiner mbx0009 at yahoo.com
Thu Jan 22 23:17:35 CET 2004

dear Berk
thanks for your comments ...

> [...] I also changed some of the constraint code.
> I have updated the manual for these changes.

talking about manuals, I just tried umbrella sampling
with gmx-3.2beta. Problem is both the format of the
input (pull.ppa) as well as the output (pullout.ppa)
seem to have changed, are these changes documented anywhere ?
The most recent manual available on the gmx homepage
seems to be 3.1.1 ... there was also no updated manual
in the gromacs-3.2beta.tar.gz i downloaded ...
I think I managed to sort out the correct in- and output
formats, but I'd appreciate to get some confirmation ...

I looked at the source and found that if
I only want to restrain one (the z) dimension
the  input is apparently supposed to look like:

runtype = umbrella
verbose = no
group_1 = ped
reference_group = System
reftype = com_t0
pulldim = N N Y
K1 = 2000.0
pos1 = 0.0 0.0 2.03033

pos1 is the absolute position of the umbrella center
and not its relative distance to the reference group, true ?

and the output in pull.pdo is the (negative distance
between the COM of the reference group and the COM
of group 1)

is this correct ... ?


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