[gmx-users] gmx mdrun restart

[Mark Abraham]

Hi,

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.)

Mark

On Tue, Oct 18, 2016 at 4:09 PM Sailesh Bataju <thelaven at gmail.com> wrote:

> 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.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>