restart with CMAP option

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1

Dear All;

I am unsuccessfully trying to restart a simulation with CMAP option. I browsed through the mail-list and website documentation, but I was not able to find a solution. Below I provide some details of my problem, hope my email is not too long. In short:

1.-

I first successfully run a simulation with CMAP using the options:

fix cmap all cmap charmm36.cmap
fix_modify cmap energy yes
read_data sys01.data fix cmap crossterm CMAP

as it is stated in the website (http://lammps.sandia.gov/doc/fix_cmap.html). My input DATA file (sys01.data) was generated with charmm2lammps.pl and contains 3134 cmap crossterms. The cmap energy is nicely reported using the "thermo_style f_cmap".

This simulation generates two restart files during the run :

NPT01.restart1
NPT01.restart2

at the end of the run, two extra files are generated:

NPT01.restart
NPT01.data

2.-

I am trying to continue the previous run, adding more timesteps. In my configuration file, I changed the cmap options to:

fix cmap all cmap charmm36.cmap
fix_modify cmap energy yes
read_restart NPT01.restart

and get the following messages in the log file:

Unused restart file global fix info:
fix style: cmap, fix ID: cmap
Unused restart file peratom fix info:
fix style: cmap, fix ID: cmap

The CMAP documentation states that :

"This fix writes the list of CMAP crossterms to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion."

However, after reading the read_restart website (http://lammps.sandia.gov/doc/read_restart.html), I was not able to find the options needed.

For now, my only solution is to restart from the DATA file generated in the previous simulation (NPT01.data). However, this discard the purpose of the restart files, and it would be useless if the computer is down before the simulation finishes.

Any suggestion is welcome.

Regards;

Eduardo

2

Dear All;

I am unsuccessfully trying to restart a simulation with CMAP option. I
browsed through the mail-list and website documentation, but I was not
able to find a solution. Below I provide some details of my problem, hope
my email is not too long. In short:

​[...]

​

I am trying to continue the previous run, adding more timesteps. In my
configuration file, I changed the cmap options to:

fix cmap all cmap charmm36.cmap
fix_modify cmap energy yes
read_restart NPT01.restart

and get the following messages in the log file:

Unused restart file global fix info:
  fix style: cmap, fix ID: cmap
Unused restart file peratom fix info:
  fix style: cmap, fix ID: cmap

The CMAP documentation states that :

"This fix writes the list of CMAP crossterms to binary restart files. See
the read_restart command for info on how to re-specify a fix in an input
script that reads a restart file, so that the operation of the fix
continues in an uninterrupted fashion."

However, after reading the read_restart website (
http://lammps.sandia.gov/doc/read_restart.html), I was not able to find
the options needed.

​there are no special options needed. however the logic employed in
restoring state of fixes after a restart requires that the fix is
respecified *after* the restart is read. for most fixes that is enforced,
because they must not be specified before a simulation box is (re-)created.
however fix cmap is an exception, since it has to be defined before the box
is generated in order to be able to read information from data files. so if
you move your read_restart command a few lines up, it should magically work
again.

axel.​

3

it worked. many thanks!

Eduardo