[gmx-users] funny zero-step mdrun results in 4.0.3
Berk Hess
gmx3 at hotmail.com
Wed Feb 11 18:24:40 CET 2009
Hi,
I added a format check for 4.0.4.
Berk
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] funny zero-step mdrun results in 4.0.3
Date: Wed, 11 Feb 2009 18:08:43 +0100
Hi,
It is slightly more subtle.
The spacing of the decimals points is correct,
but the last digit of x and y ends up in y and z.
Berk
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] funny zero-step mdrun results in 4.0.3
Date: Wed, 11 Feb 2009 18:01:31 +0100
Hi,
I just had a look at the gro files you mailed.
They have one space too little between the x and y columns and
the y and z columns. Or stricktly speaking according to the format,
the space between the x and y decimal point does not match the
space between the y and z decimal point.
I will add a check for this.
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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