[gmx-users] looks like a bug to me ...

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 12 14:13:01 CET 2003

On Thu, 11 Dec 2003, m b wrote:

>I used a shifted VdW potential (vdwtype = shift). In this case 
>Gromacs uses the tabulated VdW function and NOT the built-in routine
>as I would have expected. In my table file I had a value of 1.0 for all r 
>for all dispersion and repulsion terms which of course gives strange 
>results. (would changing the according code be easy ?)
>If I use vdwtype = cut-off, the system again behaves well, both with 
>the table6-12.xvg as well as with my self-made table file ... 
how do you know that it uses the table? It will make a new table if all is 
well. If you run mdrun -debug it will write out the table functions. 
Furthermore there is something strange withthe shift function, in 
particular when shifting over only .1 nm. Check the rtab.xvg and 
dtab.xvg files. (repulsion and dispersion)

>Generated table with 1000 data points for LJ6Shift.
>Tabscale = 500 points/nm
>Generated table with 1000 data points for LJ12Shift.
>Tabscale = 500 points/nm
Here it says the tables are generated rather then read from file.

>           Step           Time         Lambda      Annealing
>              0        0.00000        0.00000        1.00000
>   Energies (kJ/mol)
>           Bond          Angle    Proper Dih.          LJ-14     Coulomb-14
>    3.41280e+00    6.29621e+00    3.11374e+01   -7.44360e+00   -2.48470e+01
>        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
>    4.80048e+13    5.33325e+15    5.38126e+15    3.49249e+30    3.49249e+30
>    Temperature Pressure (bar)
>    1.75020e+31    6.75544e+29
>While with "vdwtype=cut-off" the energies and tmeperature look perfectly
>normal (i.e. much lower).
>The strangest thing is yet to come: I get exactly the same output,
>including the Coulomb (SR)-term, in md.log when I use the table6-12.xvg 
>file or a self made table file with the same VdW values as in table6-12.xvg 
>but with a (quite) different electrostaic potential. The ONLY difference 
>I find in the two log files are the Coulomb-14 terms ... 
>(again, with "vdw-type=cut-off" the Coulomb energies are quite 
>different in the two cases but always look reasonable)
>Apparently strange things are going on when one combines tables
>and vdwtype=shift ... I dread going into the code myself, done so 
>before, always gives me a headache ...   ;)
>no offense meant, Gromacs is a marvellous program, the best MD 
>package out there IMHO, and I've seen a few ...
>thanks in advance for any comments/suggestions!
>ps: another (un-related) thing that looks bug-ish:
>when a considerable part of the system is frozen I always
>end up with ridiculously high starting temperatures (>10000 K)
>when I say "gen_vel = yes" and "gem_temp = 300.0".
>I get around this by simple saying something like: "gen_temp = 0.1"
>but its still a bit worrying, possibly the reduced degrees of freedom 
>are not accounted for consistently ...
>Do you Yahoo!?
>New Yahoo! Photos - easier uploading and sharing.
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list