Hi, sorry for the late answer. But there is a completely new g_wham in the most recent gmx version 4.xx. With this one, the error
"This does not appear to be a valid pdo file" does not occur any more. And the new g_wham provides a lot of new featues, too. Best, Jochen anirban polley wrote: > Hi all, > Could you please tell me why g_wham does not give the correct > result? After doing umbrella sampling with mdrun, I got the .pdo file which > is like > > # UMBRELLA 3.0 > # Component selection: 0 0 1 > # nSkip 1 > # Ref. Group 'DPP' > # Nr. of pull groups 1 > # Group 1 'PIP' Umb. Pos. 3.388542 Umb. Cons. 100.000000 > ##### > 0.000000 1.650988 > 0.002000 1.650989 > 0.004000 1.651020 > 0.006000 1.651055 > 0.008000 1.651139 ......... > > Now, when I try to analysis it by g_wham, I have stuck. Could > you please tell me the right method? > 1. g_wham -max 1.7779 -min .8988 -temp 310 -o pull_pip2_dppc.pdo. > The error message is: > ------------------------------------------------------- > Program g_wham, VERSION 3.3.3 > Source code file: gmx_wham.c, line: 313 > > Fatal error: > You need to specify a series of pdo files as input > ------------------------------------------------------- > Question: How can I get the series of pdo file? Did it mean that I have to > vary the Umb. const. and run it many times and get many .pdo files? > > > 2. g_wham pull_pip2_dppc.pdo -max 1.7779 -min .8988 -temp 310 -o -hist > The error is : > > Opening file pull_pip2_dppc.pdo. > > gzip: stdin: not in gzip format > > ------------------------------------------------------- > Program g_wham, VERSION 3.3.3 > Source code file: gmx_wham.c, line: 89 > > Fatal error: > This does not appear to be a valid pdo file > ------------------------------------------------------- > > 3. Now, I tried it by converting .gz file as an input > > g_wham pull_pip2_dppc.pdo.gz -max 1.7779 -min .8988 -temp 310 -o > > The error is: > Opening file pull_pip2_dppc.pdo.gz. > > ------------------------------------------------------- > Program g_wham, VERSION 3.3.3 > Source code file: gmx_wham.c, line: 89 > > Fatal error: > This does not appear to be a valid pdo file > ------------------------------------------------------- > > > Could you please tell me why it gives error again and again? What is the > wrong that I have done? How Can I get the correct answer? > > Please, tell me the answer? I am eagerly waiting for your advise. > Regards, > Anirban > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php