> I am a bit confused on the g_bar part, when it says -f expects multiple > dhdl files. Do we need to run still multiple independent simulations > using different foreign_lambda values? I do not see why we should run > independent simulations, if we use for couple-lambda0 and couple-lambda1 > vdw-q and none respectively. >
As Justin said, you do need multiple simulations. That is because you need overlap between state lam_i lam_j to sample and estimate the dG efficiently . If you only have two states, lambda 0 and 1 you will most probably have a very poor overlap and therefor a poor dG estimate. g_bar expects you to provide a set of dhdl (with -f) or edr (with -e) files corresponding to you individual simulations at the chosen lambda values and for every lambda it needs the foreign lambdas provided in the mdp file. -- Szilárd > -----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 1:36 PM > To: Gromacs Users' List > Subject: Re: [gmx-users] no output dgdl file > > > > Emanuel Birru wrote: >> 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 > > This is certainly a viable method, but it is thermodynamic integration, > not BAR. > The purpose of lambda/foreign_lambda is to use the BAR method. > >> 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 > > It has always been my experience (in versions 3.3.3 and 4.5.3) that if > the free > energy code is activated, this file is written. I never specify the > file names > independently. > >> 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 > > If you suspect a bug, you should report it. If you don't use > foreign_lambda, > you can't use the BAR method. You're doing TI, not BAR. They are > fundamentally > different, and the analysis for TI is done independently of any Gromacs > tool. > >> 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. >> > > Version 4.5.3 has worked just fine for all free energy calculations I > have done. > Perhaps BAR can be done with a single simulation and multiple > foreign_lambda, > but that was not my understanding of the proper procedure (based on some > posts > by developers a few months ago). Multiple simulations, each at "native" > lambda, > are conducted with values of foreign_lambda above and below the native > value at > some lambda spacing (except for end points). Invoking g_bar gives the > total > DeltaG over all lambda intervals according to the BAR algorithm. > > -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 12:54 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 > -- 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
