> Hi Justin, >> > I was looking all the time for a file with dgdl extension throughout the directory. IIRC in previous versions -dgdl would generate such extension. I found now .xvg file which has dhdl data. (if I am right dgdl is the very dhdl in 4.5.3!)
> 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). >> >> > How long has the simulation been running? Output is buffered, and I find > that dhdl.xvg is not updated often. > > > 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 >> > > Note that turning off all interactions simultaneously (especially when > using soft-core) can be very unstable. You should (de)couple vdW and > Coulombic interactions separately. > Yes I read your comment about decoupling separately earlier on but I was not sure if this could depend upon the system so I was thinking of comparing results from two trials: trial 1: couple-lambda0 = vdw-q couple-lambda1 = none trail 2 A: couple-lambda0 = vdw-q couple-lambda1 = vdw trail 2 B couple-lambda0 = vdw couple-lambda1 = none So: 1- Does this decoupling issue depend on the system or it is a must for all FE studies? 2- I actually went through many of FE posts and never found how separete decoupling can be done. from trail 2 A and B I get dgdl files but how to get total vdw-q to none from these two? Please shed some light on the details of procedure.. 3- With free_energy turned off my runs take only a few hours but as I shift to free_energy = yes, runs take nearly one day foe each lambda.. Is this normal for s system having 2500 atoms? Thanks > >> >> 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 >
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