Hi Justin, It good that the issue is solved. As per my experience if you want to do a series of simulations it is not necessary to use foreign_lambda, for each simulation we can give different lambda values starting from 0 to 1( from fully interactive to non-interactive) no need of foreign_lamda and certainly no need of generating dhdl.xvg to calculate FE. I think -dhdl is an optional it will not be generated just because "free_energy = yes" is present. The problem with the 4.5.3 is not the problem of generating dhdl data by using single simulation with all foreign_lambda values. The problem is with g_bar, when I tried to analyse the dhdl.xvg output (with all the necessary data in it) using g_bar, it doesn't function properly. The error is related with the source code. I guess the main advantage of using 4.5.3 to calculated FE using foreign_lambda was to avoid running series of independent simulations. May be it is solved on the newer version 4.5.4., didn't try it yet.
Cheers, -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:54 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: > 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 You can do a series of simulations at many values of lambda, each specifying their own foreign_lambda. It seems to me that this method would be more reliable, but I have not tested simply attempting a single simulation with all values of foreign_lambda. Using delta_lambda is (from all that I have read) not reliable, as there are known issues with "slow growth" methods. > file names but it also generate all the necessary files including the > xvg's without the need of using -dhdl. > Whether or not one specifies -dhdl or -deffnm is independent of whether or not dhdl.xvg (or whatever name) is written. It is controlled purely by the presence of "free_energy = yes" in the input file. > I would appreciate if you come up with a new solution for him. > As reported by the OP, this issue had been effectively solved already: http://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html -Justin > Cheers > > -----Original Message----- > From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] 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:* gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Moeed >> *Sent:* Thursday, 24 March 2011 4:13 AM >> *To:* gmx-users@gromacs.org >> *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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
