[gmx-users] continuing run with tpbconv

[David van der Spoel]

On Tue, 2002-07-02 at 05:16, prakash sista wrote:
> 
> Hello all,
> 
> I am doing the simulation of a pentapeptide for one nano second. 
> In between there is a power failure and the simulation stopped in 
> the middle and when I try to resume it using tpb conv I got the 
> following error.
> 
> READING COORDS, VELS AND BOX FROM TRAJECTORY after_md.trr...
> 
> trn version: GMX_trn_file
> Read frame    962: step 240000 time  480.000Fatal error: Can not 
> determine precision of trn file, quit!
> 
> The command I used was:
> tpbconv -s after_md.tpr -f after_md.trr -o extend.tpr -extend 
> 1000
> 
> But I did one thing. I used the following command:
> tpbconv -s after_md.tpr -f after_md.trr -o extend.tpr -time 480
> 
> It did work fine. But, the problem is the earlier trr file had 
> steps upto 240730 (remember 240000 steps corresponds to 480 ps). 
> Now when I try to concatenate these two files with trjcat, will 
> the additional 730 steps (whose precision could not be determined) 
> that were done in the first step be taken care of. Or is there any 
> other method to continue the file if the
> last coordinates are not written

You have one half frame in your trajectory.
You have to repair your trj before trjcatting. Easiest is probably using
trjconv to copy it to a new file (until 480 ps only).
.
> 
> Regards
> Prakash sista
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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