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

Berk Hess gmx3 at hotmail.com
Wed Feb 11 17:54:24 CET 2009 

Hi,

I checked the gro manual page:
http://www.gromacs.org/documentation/reference_4.0/online/gro.html
and found out that it is actually pretty clear.
Note that it is fixed format, but with flexible precision which is derived
from the space between the decimal points.

I found out a while ago that in 3.3 gro was not read fixed format,
but in some messy way which was close to free format for the coordinates.
For 4.0 I changed the reading so it is really fixed format and one
can store coordinates of 1000 nm or larger and -100 nm and smaller.

Note that the different precision gro files do not adhere to the original
GROMOS format and might not be read correctly by some software.

Berk

> Date: Wed, 11 Feb 2009 10:46:26 -0600
> Subject: Re: [gmx-users] funny zero-step mdrun results in 4.0.3
> From: dmobley at gmail.com
> To: gmx-users at gromacs.org
> 
> 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.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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