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

[Xiaobing Feng]

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?
   
  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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