[gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro

[David van der Spoel]

Xiaobing Feng wrote:
> David,
>  
> Thank you, you are exactly right. The .xtc file was written with precision
> 10000. Does this mean that mdrun can use the same precision as shown
> in .gro file, or only use f8.3 as input?

For some reason trjconv writes out the gro file with the same precision 
as the input xtc file, however, this makes the file incompatible, so 
it's not a good idea really. You do however get the same precision with 
a pdb file (without velocities) or better with a g96 file (with velocities).

>  
> Xiaobing 
>  
> 
> --------------------------------
> 
>     *//*
>     Message: 5
>     Date: Fri, 03 Mar 2006 19:12:43 +0100
>     From: David van der Spoel
>     Subject: Re: [gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o
>     180ps.gro
>     To: Discussion list for GROMACS users
>     Message-ID: <4408871B.5090102 at xray.bmc.uu.se>
>     Content-Type: text/plain; charset=UTF-8; format=flowed
> 
>     Xiaobing Feng wrote:
>      > Dear everyone,
>      >
>      > I wanted to extract a frame from traj.xtc file
>      > to start a new run with different .mdp file.
>      >
>      > I ran
>      > trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro
>      >
>      > No problem, the .gro file was created, however, the
>      > format seems wrong. It uses f9.4 for the coordinates,
>      > instead of f8.3 as told in the manuel, so this gave
>      > error message when I ran grompp_d.
>      >
> 
>     could it be that you have written the xtc file with a precision of
>     10000 ?
> 
> 
> 
>      > "trjconv" generated the same output. I'm using Gromacs 3.3.
>      >
>      > The head part is as follows
>      >
>      > Generated by trjconv : SCN fluctuation t= 180.00000
>      > 18432
>      > 1SCN N 1 0.1511 -0.0590 0.3121
>      > 1SCN C 2 0.1039 -0.0360 0.2088
>      > 1SCN CH2 3 0.0430 -0.0150 0.0801
>      > 1SCN CH2 4 0.0490 0.1360 0.0500
>      > 1SCN C 5 0.1858 0.1779 0.0350
>      > 1SCN N 6 0.2932 0.2211 0.0280
>      >
>      >
>      > Any idea how to fix it? Many thanks in advance.
>      >
>      > Yours,
>      >
>      > Xiaobing
>      > 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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