You're doing too much work. If you want appending (and generally you
should, because all of our checks stop you making several of the many
available silly errors :-) ), don't name each stage differently. Once
you've forced it to write .edr files that are separate, then you have to
use the concatenation tools, and that gets you a naive concatenation.
(Though I suspect mdrun -append will still give you these extra frames,
because the previous -maxh meant that a checkpoint and an energy frame got
written at that arbitrary point of the simulation.)
On Tue, Oct 18, 2016 at 4:09 PM Sailesh Bataju <thela...@gmail.com> wrote:
> I'm following tutorial of "Lysozyme in Water" and playing with mdrun,
> restarted several times as an experiment and got confusion whether the
> restart process may have effect on subsequent process.
> Here is what I did.
> Suppose nvt.tpr file is generated then
> 1st: gmx mdrun -deffnm nvt -v -maxh 0.05
> the process goes on and stops at some point. Next i restarted it
> 2nd: gmx mdrun -s nvt.tpr -cpi nvt.cpt -deffnm nvt2 -v -maxh 0.05 -append
> the process goes on and stops. Again I restarted it
> 3rd: gmx mdrun -s nvt.tpr -cpi nvt2.cpt -deffnm nvt3 -v -maxh 0.05 -append
> the process goes on and stops.
> Then i combined all those .edr files via
> 4th: gmx eneconv -f nvt.edr nvt2.edr nvt3.edr -o nvt_comb.edr
> After that i want to generate temp_comb.xvg file
> 5th: gmx energy -f nvt_comb.edr -o temp_comb.xvg
> And i got this
> 6th: vi temp_comb.xvg
> # This file was created Tue Oct 18 19:36:56 2016
> # Created by:
> # :-) GROMACS - gmx energy, VERSION 5.1.4 (-:
> # Executable: /usr/local/gromacs/bin/gmx
> # Data prefix: /usr/local/gromacs
> # Command line:
> # gmx energy -f nvt_comb.edr -o temp_comb.xvg
> # gmx energy is part of G R O M A C S:
> # GROningen MAchine for Chemical Simulation
> @ title "GROMACS Energies"
> @ xaxis label "Time (ps)"
> @ yaxis label "(K)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Temperature"
> 0.000000 300.157532
> 1.000000 295.876801
> 2.000000 302.064392
> 3.000000 298.937622
> 4.000000 301.033997
> 5.000000 299.731812
> 6.000000 299.529449
> 7.000000 298.454712
> 8.000000 302.686157
> 8.800000 299.580170
> 9.000000 301.788818
> 10.000000 301.024384
> 11.000000 299.444427
> 12.000000 300.694550
> 13.000000 299.234558
> 14.000000 295.608673
> 15.000000 301.074036
> 16.000000 301.199493
> 16.560000 296.513916
> 17.000000 297.886108
> 18.000000 300.328278
> 19.000000 298.618591
> 20.000000 300.199432
> 21.000000 299.382965
> 22.000000 299.846497
> 23.000000 301.105682
> 24.000000 298.529266
> 24.840000 299.471161
> We see at 8, 16 and 24. They are repeated. So my question is does this
> affect the whole subsequent process in simulation. Not only the
> temperature others may have repeated too if see it thoroughly. I
> didn't see the use of -append flag from 1 & 2 step because it looks
> they are repeated anyhow.
> Thank you for your consideration.
> Self-reliant is the great potential for success.
> Gromacs Users mailing list
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