fix gcmc with shake in 13April 20117 Lammps version


I am trying to run a gcmc simulation for TIP4P/2005 water. As suggested in the manual bond lengths and the angle in water molecules are held fix with fix shake.

I am unsure of whether I should use the following command:

fix_modify constrain dynamic/dof no

in analogy to the CO2 example provided, which was constrained with rigid/small. However, I can say that I get exactly the same results regardless of whether I use this command or not.

The problem is that after a number of steps (that varies depending on the particular conditions chosen to perform the simulation), the code stops printing data and keeps hanging for ever as it were running an infinite loop. The job does not exit, neither prints an error message. It just hangs there forever.

Curiously the very same input files (with a minor change in the “compute_modify thermo_temp dynamic yes” to adjust to the previous synthax) with a previous lammps version (22 Nov 2016) seems to be running “properly” (it completed the whole simulation without printing weird numbers, although I have not checked that the results match calculations with other codes).

According to the manual I should be able to use shake with gcmc. So I guess there might be something wrong either in my in.gcmc.tip4p2005 file or in my molecule definition (h2o.txt), but after reviewing several times, I do not see what can be wrong.

Any help would be very much appreciated.



h2o.txt (675 Bytes)

in.gcmc.tip4p2005 (2.35 KB)

log.lammps.gz (79.5 KB)

You are the second person this week to use fix shake with fix gcmc, but without a fix that actually performs the time integration, such as fix nve or nvt. you can’t do SHAKE without a time integration scheme. It is true that the fix shake doc page does not mention this, but it should be pretty obvious. Please study examples/peptide to see how to use SHAKE.