[gmx-users] funny zero-step mdrun results in 4.0.3

[David Mobley]

David,
> Both your gro files are wrong, the definition of gro files has never
> changed. Do you mean to say this has ever worked?

Yes, it worked fine in 3.3.x. I would point out that trjconv has an
-ndec option which, if used to output a gro file, will generate
high-precision gro files as output. Presumably these are acceptable
gro files?!?

What exactly is wrong with it?

Here's one that works (an output with -ndec from trjconv); I'm not
clear on why this one works and the one I sent doesn't:

Generated by trjconv : 9 system in water t=   0.00000
   17
    1ASN     C4    1  20.166000366211  20.479019165039
20.427963256836  0.0000000000000  0.0000000000000  0.0000000000000
    1ASN     H1    2  20.146055221558  20.570739746094
20.372158050537  0.0000000000000  0.0000000000000  0.0000000000000
    1ASN     H2    3  20.098955154419  20.395944595337
20.404985427856  0.0000000000000  0.0000000000000  0.0000000000000
    1ASN     H3    4  20.166000366211  20.499057769775
20.535308837891  0.0000000000000  0.0000000000000  0.0000000000000
    1ASN     C7    5  20.295000076294  20.426000595093
20.385000228882  0.0000000000000  0.0000000000000  0.0000000000000
    1ASN     O1    6  20.315000534058  20.309999465942
20.349000930786  0.0000000000000  0.0000000000000  0.0000000000000
    1ASN     N2    7  20.393997192383  20.515981674194
20.393993377686  0.0000000000000  0.0000000000000  0.0000000000000
    1ASN     H4    8  20.489086151123  20.482969284058
20.386993408203  0.0000000000000  0.0000000000000  0.0000000000000
    1ASN     H5    9  20.374940872192  20.611291885376
20.421081542969  0.0000000000000  0.0000000000000  0.0000000000000
    2SOL     OW   10  20.548002243042  20.120998382568
20.291999816895  0.0000000000000  0.0000000000000  0.0000000000000
    2SOL    HW1   11  20.500000000000  20.046926498413
20.254966735840  0.0000000000000  0.0000000000000  0.0000000000000
    2SOL    HW2   12  20.479961395264  20.183086395264
20.318038940430  0.0000000000000  0.0000000000000  0.0000000000000
    2SOL     MW   13  20.535623550415  20.119720458984
20.290826797485 -0.0009536742582  0.0000000000000  0.0000000000000
    3SOL     OW   14  20.242019653320  20.178009033203
20.123998641968  0.0000000000000  0.0000000000000  0.0000000000000
    3SOL    HW1   15  20.164087295532  20.143032073975
20.167186737061  0.0000000000000  0.0000000000000  0.0000000000000
    3SOL    HW2   16  20.300615310669  20.201835632324
20.195838928223  0.0000000000000  0.0000000000000  0.0000000000000
    3SOL     MW   17  20.239955902100  20.176818847656
20.136268615723 -0.0085830679163 -0.0038146970328  0.0000000000000
  40.642551422119  40.642551422119  40.642551422119


Maybe this is just wishful thinking, but it would be nice if the
manual actually explained the specifications of the gro file format.
For example, it is clearly not fixed-width, as the number of digits in
the columns can vary, but at the same time it doesn't appear to be
tab/space delimited, as the columns of velocities can occasionally run
together (if I'm using the -ndec option, especially). Obviously one
can look at the code (perhaps I should do this) but it seems it should
be documented.

Thanks,
David



> If you want high precision use g96.
>
>>
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> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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