[gmx-users] gmx mdrun restart

[Sailesh Bataju]

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.