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CHARMM constrained QM/MM dynamics crashes
#38182 01/29/21 03:01 AM
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I am trying to run a constrained walk simulation for committor analysis of transition path ensembles. I constrain the QM atoms as well as some of the residues
interacting with it using "cons harm force" and run the dynamics, and this calculation starts to become erratic within few steps and crashes. I have attached the
input and the output files here. I would appreciate any help that can make me understand this crash and fix it. Thanks!

Attached Files
consw_inp.txt (1.76 KB, 21 downloads)
SHA1: 0769549639e2bc1f689d8053c9a2e55d817ae5e5
cw_out.txt (177.16 KB, 23 downloads)
SHA1: 7f4bc7393fbd46998c2bb2cce4ff7714ca8d6ab5
Re: CHARMM constrained QM/MM dynamics crashes
sreeganb #38184 01/30/21 08:06 PM
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rmv Online Content
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I have to say that I've never used any of the QM/MM methods myself, so I cannot comment on the QM setup.

However, I've noticed a few things in the output log that may be relevant.

First, the CONS HARM command may need to follow the reading of the coordinates from ts254.crd, esp. if the restrained coordinates are significantly different from those in the initial coordinates read earlier in the script.

Second, at dynamics startup the message

**** Warning **** The following extraneous characters
were found while command processing in DCNTRL
TREF 300


indicates a failed attempt to establish a thermostat. That is the T setting for the weak coupling (Berendsen) thermostat, which is known to be flawed; it gives a T distribution which is significantly narrower than a proper Boltzmann distribution, and its usage is deprecated. The TCONS and TCOUPLE keywords are also required for that thermostat.

Third, I note there are no boundary conditions of any kind. While this may not a huge issue with the QM part, there are known artifacts from the particle:vacuum interface present for a system with no periodic boundary conditions. The more rigorous Hoover thermostat requires the use of periodic boundary conditions via CRYSTAL commands.


Rick Venable
computational chemist

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Re: CHARMM constrained QM/MM dynamics crashes
rmv #38227 03/25/21 06:44 AM
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Thanks! That worked like a CHARMM! I just had to move the CONS HARM after reading the coordinates step.


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