[gmx-users] continuing run with tpbconv
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jul 2 23:19:55 CEST 2002
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
> 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).
> Prakash sista
> There is always a better job for you at Monsterindia.com.
> Go now http://monsterindia.com/rediffin/
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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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