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<font size="2">Hi, Mark
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> tc-grps             =  A-chain B-chain drug SOL  NA+
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This is bad - see <a target="_blank" href="http://www.gromacs.org/Documentation/Terminology/Thermostats">http://www.gromacs.org/Documentation/Terminology/Thermostats</a>
<br />Thank you for your website.  I understand now.
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> grompp -f md2.mdp -n index.ndx  -p topol.top -c ${n-1}ps.gro  -t
${n-1}ps.trr -o ${n}ps.tpr
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> mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
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You are following neither of the approaches recommended here <a target="_blank" href="http://www.gromacs.org/Documentation/How-tos/Doing_Restarts">http://www.gromacs.org/Documentation/How-tos/Doing_Restarts</a>
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<br />Ya, I'm sorry but my colleborator give me that before.
<br />It is similiar to the commends connect position restrained dynamics and MD.
<br />You can find grompp read gro and trr of last time frame to make a tpr file of next time frame.
<br />I thought this cause the time write on each snapshot is 0, but the dynamics is still processing.
<br />Did I miss something?
<br />You say the pressure-coupling will be lost in each ps, does it mean that trr file doesn't have this message inside?
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> Theses two data generated by different ways are totaly different.
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> Here I mean different is not on the number buy mean the tendency of figure.
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See <a target="_blank" href="http://www.gromacs.org/Documentation/Terminology/Reproducibility">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a>
<br />Ya, I know this since last time you show me this web in mailing list.
<br />Thank you again.
<br />But the different between these two outputs is totaly different.
<br />I have four systems with different parameter gen_seed.
<br /></font><font size="2">First is always unstable and irregular, but second is stable and regular.</font><font size="2">
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> On the contrary, the second method generate a stable movie and fluctuation
of interaction energy.
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> Theotically these two should be the same, right?
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The second is probably happier about not losing the pressure-coupling
information every 1ns. However only much
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much longer trajectories should show mutual convergence, and the movie is not a
reasonable way to look for it.
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Mark
<br />Sorry I don't understand you here.
<br />Do you mean second way seems to more correct?
<br />And what kind of mutual convergence you mean here?
<br />Does It mean I can try to find mutual convergence in output of second way?
<br />I'm sorry for my stupid and poor English.
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<br />Sincerely yours,
<br />Hsin-Lin
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