[gmx-users] Translating my system using editconf causes my run to crash!

[S. Alireza Bagherzadeh]

Dear Mark,




> Today's Topics:
>
>
>    4. Translating my system using editconf causes my run to     crash!
>       (S. Alireza Bagherzadeh)
>    5. Re: Translating my system using editconf causes my run to
>       crash! (Mark Abraham)
>
>
>
> ----------------------------------------------------------------------
>
>
> Message: 5
> Date: Tue, 5 Feb 2013 22:21:05 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> Subject: Re: [gmx-users] Translating my system using editconf causes
>         my run to       crash!
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CAMNuMAT6ofqGeJGGGNJ6KEhM++e5XKBf_w4kfPEfmcOJL=
> vPvA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Feb 5, 2013 at 10:05 PM, S. Alireza Bagherzadeh <
> s.a.bagherzadeh.h at gmail.com> wrote:
>
> > Hi everyone,
> >
> > I am using "editconf" to translate my system along the z-axis.
> >
>
> Why? mdrun doesn't care.
>

Because I want to preserve the geometry of my system for the purpose of
visualization as well as some post-analysis code that I write.
I noticed that mdrun as an output gives an image of the simulation box that
sits on the origin and extends along the positive direction of the
coordinate axises.

This might clarify what I mean:

My initial configuration looks like this:

GAS | WATER | ICE | WATER | GAS       (center of system at z-axis: z = 35
nm)

My final configuration looks like this:

TER | ICE | WATER | GAS GAS | WA        (center of system at z-axis: z =
dZ/2 = 14.32431)

dZ is the simulation box length along the z-axis.



> However, by trial and error I realized that only at some values of the
> > z-component of the translation vector I am able to run my system,
> otherwise
> > my run produces a number of stepN.pdb files with the following output:
> > ---------
> > Getting Loaded...
> > Reading file topol.tpr, VERSION 4.5.5 (single precision)
> > Loaded with Money
> >
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> >
> > Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#
> >
> > Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
> > Wrote pdb files with previous and current coordinates
> > starting mdrun 'Methane hydrate between 2 silica surfaces in contact with
> > water and gas'
> > 500000 steps,    500.0 ps.
> > Shake did not converge in 1000 steps
> >
> > Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#
> >
> > Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
> > Wrote pdb files with previous and current coordinates
> > step 0Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > ....
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > step 100, will finish Thu Feb  7 12:49:37 2013Shake did not converge in
> > 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > ...
> >
> > [So, I do Ctrl+C to break the run]
> >
> > Received the INT signal, stopping at the next NS step
> >
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > step 300, will finish Thu Feb  7 13:12:45 2013Shake did not converge in
> > 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > Shake did not converge in 1000 steps
> > Wrote pdb files with previous and current coordinates
> > step 310, will finish Thu Feb  7 13:16:46 2013
> >                NODE (s)   Real (s)      (%)
> >        Time:    104.820    106.221     98.7
> >                        1:44
> >                (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> > Performance:     21.511      1.739      0.256     93.623
> > --------
> >
> > I am using this command:
> > editconf -f conf.gro -translate 0 0 Vz -o conf-translated.gro
> >
> > if Vz = 5, 10 or 35 -> no error!
> > if Vz = 15, 20, 25 or 35 -> error!
> >
> > I have 58883 atoms in my conf.gro file with the following simulation box:
> > 3.60900   6.60800  28.64862
> >
> >
> > This looks so strange to me! Why just translating over the z-axis causes
> > any problem in my system??!!!
> >
> > Have you ever had this experience with gormacs? Would you have an insight
> > on why this is happening?
> >
>
> The usual reasons include
>
> 1) The system is not close to equilibrium, and the new coordinates lead to
> slightly different floating-point arithmetic and chaos sometimes leads to
> integration failure
>

Can you elaborate more on this please?


> 2) You're combining the translated system with something else and
> overlaying atoms
>

I am just using "-translate"...


> 3) Your .mdp file refers to something specific about the coordinate system
> that no longer makes sense
>

Wold you please give an specific instance?


>
> Mark
>
>
>
Best regards,
Alireza