[gmx-users] Basic 3.20 beta question

Pim Schravendijk schraven at mpip-mainz.mpg.de
Mon Dec 15 12:22:01 CET 2003


I am just trying to run 320 beta next to 314 with the "water" tutorial.
Two things so far for 3.20 beta:

1. - grompp gives me a warning:

WARNING 1 [file grompp.mdp, line unknown]:
  Unknown left-hand zero-temp_time in parameter file

In my .mdp file I see:

annealing                = no
; Time at which temperature should be zero (ps) =
zero-temp_time           = 0

That doesn't look very erroneous? Maybe it should be written differently
for grompp to recognize it?

2. - I've run:

~schraven/bin/gromacs320betax86single/i686-pc-linux-gnu/bin/mdrun -s
water.tpr -o water.trr -c water_out.gro -v -g water.log

-rw-r--r--    1 schraven theorie      446K 2003-12-15 11:22 traj.xtc
-rw-r--r--    1 schraven theorie       15K 2003-12-15 11:22 water.trr
-rw-r--r--    1 schraven theorie       44K 2003-12-15 11:22 water_out.gro

My .trr file is very small, gmxdump shows me it is only the last step:

water.trr frame 0:
   natoms=       648  step=     10000  time=        20  lambda=         0

I don't understand why I would get a .xtc file, in 3.14 I don't get a .xtc
file unless I add the -x option. Is this behaviour a bug or a feature?

Thanks for the effort, hopefully this will be all now.

Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research

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