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

[David Mobley]

Berk,

> 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.

Thanks. I was looking at the 3.3 paper manual.

> 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.

OK, that's good to know.

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

Thanks,
David


> 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.
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