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

[Chenyue Xing]

Please search in the mailing list archive.
It's a problem of the g_wham and there was a fixed version from David
Bostick of Scripps.

Chenyue

On Mon, Jul 21, 2008 at 12:04 PM, crascgap <crascgap at uol.com.br> wrote:

> 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:
>
> # UMBRELLA  3.0
> # 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,
> Cristiano.
>
>
>
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