Hi,
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.
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