PMF by ColVars?

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1

Dear lammps users,

After getting not acceptable results from fix smd, I tried colvars to calculate the PMF and work of desorption of a molecule from surface through steered molecular dynamics. I established my input file using the mailing list and the lammps example for ColVars.
The problem is that:
1- The output file of ColVars after simulations only contains the number of steps and nothing else! Other lammps outputs are fine.
2- The molecule does not move from the surface to the target point specified.

The input file of ColVars is as follows. I don’t know where I am making the mistake…

Thanks a lot for your suggestions.

2

two suggestions:

  1. i see from your other posts, that you are not using a LAMMPS version from this summer. when reporting problem where LAMMPS doesn’t work as expected, always try with the very latest patch level as well (and let people know which one) to make sure that you are not reporting a problem that has already been addressed.

  2. rather than reporting a problem with a complex (production) system, try to first set up simple toy problems to test and familiarize yourself with a new code. things will be much easier and faster to test and you can simply post your complete toy inputs in case people want to reproduce your issue and track down any potential problems. in this case, it would be sufficient to simply define a single simple collective variable (e.g. distance between two atoms) in a simple test example (e.g. in.melt) and see if the colvars trajectory monitors the distance. it does for me, if i use the latest LAMMPS version (dec 24th), so there is a definite chance that you are subject to a bug that has since been fixed in a newer version of LAMMPS.

axel.

3

Hello Xiaolin: in addition to what Axel suggested, have you tried searching the mailing list for this issue? Your question was already asked and answered last 12/14/15.

Regards

Giacomo