Hi Justin, Sure what you wrote is correct, what I am trying to tell to him is that if he has more than one foreign lambda it is better to put all of them as it is not logical to use only one foreign lambda to calculate FE (0 - 0.1) and he doesn't have delta lambda too. -Deffnm is sure all about file names but it also generate all the necessary files including the xvg's without the need of using -dhdl.
I would appreciate if you come up with a new solution for him. Cheers -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: > Hi, > > > > Your foreign_lambda value is only one, please put all your lambda values > separated by space and you will get the dhdl file. And make sure that This is not required. You can specify as many or as few foreign_lambda values as you like. > you use -deffnm when you run your mdrun to get all the out put files by > default. > The -deffnm flag controls the names of the files, not which ones are written. -Justin > > > Cheers, > > > > *From:* [email protected] > [mailto:[email protected]] *On Behalf Of *Moeed > *Sent:* Thursday, 24 March 2011 4:13 AM > *To:* [email protected] > *Subject:* [gmx-users] no output dgdl file > > > > Hello, > > I have a little problem with FE output file. Below is the settings and > also I am including -dgdl in the command I issue but no dgdl (or dhdl) > file generates. I dont figure where the problem lies ! (version 4.5.3). > > free_energy = yes > init_lambda = 0 > delta_lambda = 0 > sc_alpha = 0.5 > sc-power = 1 > sc_sigma = 0.3 > foreign_lambda = 0.1 > dhdl_derivatives = yes > couple-moltype = Polymer > couple-lambda0 = vdw-q > couple-lambda1 = none > couple-intramol = yes > nstdhdl = 10 > separate_dhdl_file = yes > dh_hist_size = 0 > dh_hist_spacing = 0.1 > > Best > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
