[gmx-users] Basic 3.20 beta question

[David van der Spoel]

On Mon, 2003-12-15 at 12:21, Pim Schravendijk wrote:
> Hi,
> 
> 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:
> 
> ; SIMULATED ANNEALING CONTROL =
> 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?

Yes, the syntax for annealing has changed, check your mdout.mdp

We should probably go over the tutorial before release.

> 
> 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.

You get an xtc file if nstxtcout in the mdp file is non zero. I don't
recall this feature having changed, but maybe the input file has...


> 
> --
> Pim Schravendijk - PhD Student
> Max Planck Institute for Polymer Research
> http://www.mpip-mainz.mpg.de/~schraven/
> 
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-- 
David.
________________________________________________________________________
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
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