FAQ_running

Frequently asked questions at running the erdst program

Program fails to run with an error message: "Error: cannot find plugin paths, please set ERMOD_PLUGINS environment variable"

This error occurs when either:

• You forgot to perform "make install"
• "make install" failed and you ignored the error message.

Try to do "make install" (also see the section of "make install fails ..." on Frequently asked questions at the installation).
If you do not want to install programs, you can also specify the directory of plugin files (.so files) to ERMOD_PLUGINS.

If you want to do so and are using sh, bash or zsh,

::::sh
export ERMOD_PLUGINS=(path to the ERmod source-code directory)/vmdplugins/libexec

If you are using csh or tcsh,

::::csh
setenv ERMOD_PLUGINS (path to the ERmod source-code directory)/vmdplugins/libexec

The command should be executed every time before you execute ermod.

Calculation stops with "The minimum of the energy coordinate is too large".

See The minimum of the energy coordinate is too large.
The following description is valid only when user uses ver 0.2.x of ERMOD with gromacs or uses ver 0.3.x of ERMOD with gromacs or AMBER.

Since ermod uses a set of predefined bin width and size for storing interaction energies, the interaction energy between solute and solvent may be lower than the minimum energy bin.
This problem typically happens with highly charged ion.

To extend the bin size to lower energy, pass --minenergy energy option to gen_input.
The energy should be chosen so that it is small enough.
A general guideline is that for an ion of total charge of +/-1, --minenergy -80 will be a good starting point.
When the charge is +/-2, --minenergy -120 will be a good starting point.
For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of Parameter files for ermod.

User must specify the same energy meshes for both soln and refs parts.

uvrange.tt can be helpful when user wants to estimate the minimum energy.
This file is generated when the ermod program finishes successfully.
The uvrange.tt output looks like:

 species     minimum        maximum
    0       -0.08086        0.00799
    1      -30.66799       0.65871E+34
    2      -13.02511       0.79338E+38

In this list, the species 0 corresponds to the self-enegy of the solute. Shown are the minimum and maximum of the solute self-energy.
The self-energy is usually small in magnitude when a large MD unit cell is used.
The species 1 is the 1st solvent species, and the minimum and maximum of the pair energy between the solute and the 1st solvent species are shown.
Similarly for the species 2, and so on.
In this example, the minimum pair energy of the solute is -30.7 kcal/mol against the solvent species 1 and is -13.0 kcal/mol against the solvent species 2.

Version 0.2 stops calculation after reading long trajectory.

The problem is reported with mvapich1-1.1.
No workaround is found at this moment.
User should update mvapich (recommended to use the latest version of mvapich2).

Ermod cannot read HISTORY file if it is linked to another symbolic link

In version 1.0, this bug should have been fixed. If you encounter this bug please report to devs (at ermod-users mailing list or directly mail us).

If the HISTORY file is symlinked to ../otherdir/foo and ../otherdir/foo is further symlinked to foo2, then the program searches for foo2 in the current directory instead of ../otherdir.
This is a feature of VMD plugin-based file I/O and cannot be fixed at the moment.
A current workaround is to link the target with the absolute path.

ERmod cannot read netCDF trejectory.

The extension of the trajectory file must match ".nc" for ERmod to recognize the file as the netCDF format. Rename the trajectory file to have .nc extension.

In version 0.3, user can use "ERMOD_FORCE_PLUGIN_TYPE" environment variable to force the plugin type. For example, in sh/bash/zsh, "export ERMOD_FORCE_PLUGIN_TYPE=nc" forces ERmod to use netCDF plugin to read ALL trajectories.