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 <[EMAIL PROTECTED]> 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. > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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