Hi! When you are computing your zero-step energies, do you then start from the gro-file that you got from em? If so, maybe the energies changes because gro-files have a fixed precision format (with three decimals), while the em-calculations are done using either full single or double precision.
Your second issue is almost certainly related to rounding errors. The all-vs-all and the cutoff-code (even with enormous cut-offs) compute interactions in completely order. I would not worry about a 0.005 nm difference in RMSD. /Per 10 mar 2011 kl. 14.27 skrev Ehud Schreiber: > Dear Mark Abraham (and anyone else interested), > > I have implemented your suggestion, changing in the status.mdp file to > integrator = md and adding continuation = yes (this is the new name of > the unconstrained_start parameter); however, this did not have any > effect - the energy remained as before, different from the one obtained > during the minimization. > > I have then encountered another (perhaps related) issue. > I thought that the problem may arise from the combination of the > generalized Born and all-vs-all settings. > I have therefore changed in the minimization to rgbradii = rlist = > rcoulomb = rvdw = 100 (from = 0). > As my system is far smaller than 100 nm, I expected these parameters to > provide also an all-vs-all setting (even if non-optimized). > Nevertheless, the resulting structure differed from the previous > minimized one (rmsd ~ 0.005 nm, delta energy ~ a few kJ/mol). Can this > arise from rounding effects only or does this signify a problem? I'm not > sure what rgbradii does, but the manual states that it must equal rlist. > In addition, changing also status.mdp to have all radii = 100 and > running on the new optimized output again does not yield the same energy > as during the optimization. > > Does all of this make any sense to you? > > Thank, > Ehud. > > >> Message: 6 >> Date: Tue, 08 Mar 2011 23:37:12 +1100 >> From: Mark Abraham <[email protected]> >> Subject: Re: [gmx-users] g_energy inconsistent results >> To: Discussion list for GROMACS users <[email protected]> >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset="iso-8859-1" >> >> On 8/03/2011 9:44 PM, Ehud Schreiber wrote: >>> >>> Dear Gromacs users, >>> >>> I am working with version 4.5.3, using the opls-aa forcefield in an > implicit solvent, all-vs-all setting: >>> >>> pdb2gmx -ter -ff oplsaa -water none -f file.pdb >>> >>> I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). > >>> The last stage is the following: >>> >>> grompp -f em3.mdp -p topol.top -c em2.gro -t em2.trr -o em3.tpr -po > em3.mdout.mdp >>> mdrun -nice 0 -v -pd -deffnm em3 >>> g_energy -s em3.tpr -f em3.edr -o em3.potential_energy.xvg >>> >>> where the mdp file is: >>> >>> ;;;;;;;;;;;;;;;;;;; em3.mdp ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; >>> integrator = l-bfgs >>> nsteps = 50000 >>> implicit_solvent = GBSA >>> gb_algorithm = Still >>> sa_algorithm = Ace-approximation >>> pbc = no >>> rgbradii = 0 >>> ns_type = simple >>> nstlist = 0 >>> rlist = 0 >>> coulombtype = cut-off >>> rcoulomb = 0 >>> vdwtype = cut-off >>> rvdw = 0 >>> nstcalcenergy = 1 >>> nstenergy = 1000 >>> emtol = 0 >>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; >>> >>> The last line in the em3.potential_energy.xvg file should give the > (potential) energy of the minimized structure em3.gro . >>> >>> I wish also to compute the potential energy of .gro files in general, > not necessarily obtained from a simulation. >>> For that, I prepared a .mdp file for a degenerate energy > minimization, having 0 steps, designed just to give the status of the > file: > >> Zero-step EM does not calculate the initial energy because it is not > useful for gradient-based energy minimization. >> I don't recall the details, but perhaps the first EM step is reported > as step zero. >> Instead, you should use zero-step MD (with unconstrained_start = yes), > or (for multiple single points) mdrun -rerun. > >> You will not necessarily reproduce the g_energy energies with > anything, because the energy is dependent on the state of the neighbour > lists. >> If nstenergy is a multiple of nstlist, then those energies should be > fairly reproducible. > >> I have updated the grompp source to provide a note to the user to warn > against zero-step EM. > >> Mark > >>> ;;;;;;;;;;;;;;;;;;; status.mdp ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; >>> integrator = l-bfgs >>> nsteps = 0 >>> implicit_solvent = GBSA >>> gb_algorithm = Still >>> sa_algorithm = Ace-approximation >>> pbc = no >>> rgbradii = 0 >>> ns_type = simple >>> nstlist = 0 >>> rlist = 0 >>> coulombtype = cut-off >>> rcoulomb = 0 >>> vdwtype = cut-off >>> rvdw = 0 >>> nstcalcenergy = 1 >>> nstenergy = 1 >>> emtol = 0 >>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; >>> >>> The only changes from the former .mdp file are in nsteps and > nstenergy. >>> >>> However, when I run this potential energy status run on em3.gro > itself, >>> >>> grompp -f status.mdp -p topol.top -c em3.gro -o status.tpr -po > status.mdout.mdp >>> mdrun -nice 0 -v -pd -deffnm status >>> g_energy -s status.tpr -f status.edr -o status.potential_energy.xvg >>> >>> and look at the (single) energy line in status.potential_energy.xvg I > find that the energy does not agree with the one obtained during > minimization (it's higher by some tens of kJ/mol). >>> >>> What am I doing wrong? How should one reliably find the energy of a > given .gro file? >>> >>> Moreover, when changing in status.mdp to integrator = steep, the > results also change dramatically -- why should the algorithm matter if > no steps are performed and the initial structure is explored? >>> >>> Thanks, >>> >>> Ehud. >>> > -- > 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]. 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