Dear David and Berk,
I have performed further tests on a box of 1136 waters with one sodium atom, to see if mdrun -rerun was able to reproduce the Lennard-Jones energies calculated during the run from frames stored in an xtc trajectory. I used three .gro files with grompp :
- confin.gro, corresponds to step 0 - smallbox.gro, smaller box size - bigbox.gro, very large box sizeI checked the behavior of gromacs 3.3.0 with the bug fix provided in bugzilla (3.3.0_patch) and gromacs 3.3.1. Here are my observations:
1) Neither 3.3.0_patch nor 3.3.1 reproduce the LJ energies of the run. 2) 3.3.0_patch gives results that are independent of the .gro file.3) 3.3.1 results depend on the .gro file. A small box makes energies explode. 4) 3.3.1 with a .gro corresponding to the initial condition gives the same results as 3.3.0_patch. 5) 3.3.1 with a very large box (no interaction between images ?) gives a good correlation with the run.
I attach an eps figure illustrating the points above. The deviations between 3.3.0_patch and the energies from the run are about 8% of the total value, which can not be explained by the imprecisions of the positions in the .xtc file.
Below is the .mdp file that I used for the run. For the rerun, I changed nstlist and nstenergy to 1. I also set tcoupl and pcoupl to "no".
Tell me what you think about this. I am puzzled, especially about the behavior of 3.3.1 with confin.gro . Also point (5) above hints to the fact that LJ interactions between images are handeled wrongly by both 3.3.0_patch and 3.3.1.
Cheers, Michel ------------------------------------------------------------------------ title = Na cpp = /lib/cpp include = -I../top integrator = md dt = 0.001 nsteps = 100000 comm_mode = Linear nstcomm = 1 comm_grps = System nstxout = 10000 nstvout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc-grps = System nstlist = 5 ns_type = grid rlist = 0.8 coulombtype = reaction-field rcoulomb = 1.4 epsilon_rf = 80 vdw-type = cut-off rvdw = 1.4 tcoupl = nose-hoover tc-grps = System tau_t = 0.15 ref_t = 300 Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no gen_temp = 300 gen_seed = 173529 ------------------------------------------------------------------------
Dear David and Berk,I am investigating further to understand why I don't get the same energies with -rerun. I will report next week.Thanks for your replies, MichelI just checked the 3.3.1 source code in md.c and the box is copiedfrom the xtc file.I don't know where your problems could come from. Berk.From: "David Mobley" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Subject: Re: [gmx-users] mdrun -rerun and box size bug not fixed? Date: Thu, 1 Nov 2007 06:12:56 -0700 Dear Michel, Are you sure you're using 3.3.1? I have not checked this specific issue -- but I have checked that if I run hydration free energy calculations in patched 3.3.0, and again in patched 3.3.1, and do my usual free energy analysis using mdrun -rerun, I get the same values. That either tells me that (a) the patch is in 3.3.1 also, or possibly (b) that the problem is small enough for hydration free energies that I'm missing it. Anyway, hopefully (a) is true, otherwise I'm going to need to repeat a LOT of work (and be very grumpy). Keep me posted on this. Thanks, David
-- ========================================================== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm ==========================================================
LJ-rerun.eps
Description: PostScript document
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