[gmx-users] different output generated by continue and discontinue > simulation

[Hsin-Lin Chiang]

Hi, Mark
> > tc-grps             =  A-chain B-chain drug SOL  NA+ 
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> This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats
Thank you for your website.  I understand now.
> > 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 http://www.gromacs.org/Documentation/How-tos/Doing_Restarts 
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Ya, I'm sorry but my colleborator give me that before.
It is similiar to the commends connect position restrained dynamics and MD.
You can find grompp read gro and trr of last time frame to make a tpr file of next time frame.
I thought this cause the time write on each snapshot is 0, but the dynamics is still processing.
Did I miss something?
You say the pressure-coupling will be lost in each ps, does it mean that trr file doesn't have this message inside?

> > 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 http://www.gromacs.org/Documentation/Terminology/Reproducibility
Ya, I know this since last time you show me this web in mailing list.
Thank you again.
But the different between these two outputs is totaly different.
I have four systems with different parameter gen_seed.
First is always unstable and irregular, but second is stable and regular.
> > 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 
> much longer trajectories should show mutual convergence, and the movie is not a reasonable way to look for it. 
> 
> Mark 
Sorry I don't understand you here.
Do you mean second way seems to more correct?
And what kind of mutual convergence you mean here? 
Does It mean I can try to find mutual convergence in output of second way?
I'm sorry for my stupid and poor English.

Sincerely yours,
Hsin-Lin

 
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