Re: [gmx-users] RE: g_energy inconsistent results
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 >> Subject: Re: [gmx-users] g_energy inconsistent results >> To: Discussion list for GROMACS users >> Message-ID: <4d7622f8.7050...@anu.edu.au> >> 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 = 5 >>> 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=
[gmx-users] RE: g_energy inconsistent results
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 >Subject: Re: [gmx-users] g_energy inconsistent results >To: Discussion list for GROMACS users >Message-ID: <4d7622f8.7050...@anu.edu.au> >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 = 5 >> 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
