[gmx-users] Umbrella Sampling and .pdo format file

crascgap crascgap at uol.com.br
Mon Jul 21 21:04:45 CEST 2008

Hi everyone.

I have exactly the same problem as user VENKATESH HARIHARAN from
our gmx-user list.

I am running this command to calculate the pmf:

mdrun -s system.tpr -pi umbrella.ppa -po umbrella.1.0.0.ppa -pn index.ndx -pd umbrella.1.0.0.pdo -deffnm umbrella.1.0.0 -v &

And then I get this .pdo file:

# Component selection: 0 0 1
# nSkip 1
# Ref. Group 'POP'
# Nr. of pull groups 1
# Group 1 'Protein'  Umb. Pos. -8.028000  Umb. Cons. 250.000000
0.000000    0.182068
0.002000    0.182095
0.004000    0.182115
0.006000    0.182142
0.008000    0.182212
0.010000    0.182322
0.012000    0.182435
0.014000    0.182518
0.016000    0.182584
0.018000    0.182671
0.020000    0.182799
0.022000    0.182972
and so on...

When I try to g_wham (command line: g_wham umbrella.1.0.0.pdo -o pmf.xvg) from Gromacs 3.3 version I get this error message:

"Program g_wham, VERSION 3.3
Source code file: gmx_wham.c, line: 90

Fatal error:
This does not appear to be a valid pdo file "

I will be very disappointed if this error is due to a bug in Gromacs.
I have already tried  to run g_wham with my .pdo file gziped (.pdo.gz) and still
I get the same error msg.

Does, please, any one knows what is going on ?
What is a ".pdo VALID file format" then !!??

There is much interest in literature nowadays for pmf calculations of
biological systems !!!

So, my problem today, could be your big problem tomorrow !!
Let's try to solve this one for the goodness of this side of science.

Thank you all in advance,

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