[gmx-users] the -extend function of the tpbconv command

Acoot Brett acootbrett at yahoo.com
Wed Apr 4 02:28:47 CEST 2012

Dear All,
I have completed a 1ns production MD. Then I intended to extend it for another 1 ns.
I use command 
"tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt"
I think the results will be automatically attended to previous md_0_1.tpr and md_0_1_noPBC.xtc.
Then I use "g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" to get the rmsd.xvg file. Then I use "xmgrace -nxy potential.xvg" to display it. However I find for the  curve the x-axis is from 0 ns to 1 ns, not from 0 ns to 2 ns.
The definition of "-extend" of the command "tpbconv" is "Extend runtime by this amount (ps)". Thus the commands I used are correct.
Will you please tell me how to process for the extension MD so that the curve of the rmsd.xvg (and all the other xvg files) will have x-axis from the 0 to the 2 ns (2 ns is the total MD time, including the 1 ns extended part)?
I am looking forward to getting your reply.
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