Strange glitches when performing energy minimization in MDFF simulations

From: Tristan Croll (
Date: Sun Feb 09 2014 - 23:49:41 CST


I'm currently running simulations in which I have a protein complex fitted within a ~10A cryo-EM map, and have been running "pseudo-equilibrium" simulations (with the MDFF constant dialled all the way down to 0.005) to allow it to rattle itself down to an energy minimum with weak guidance from the map. I've found that under these conditions it seems quite safe to remove all secondary structure, cispeptide and chirality extrabonds without anything going awry - except in the specific case where I perform an energy minimization at the start of a continuation run. For some reason, during minimization small, seemingly random portions of the structure (e.g. within a sphere of ~10A diameter) will jump into crazy configurations (bond lengths and angles well away from normal) before settling back to a "standard" arrangement (except sometimes with trans to cis or chirality flips). Apart from the MDFF forces, which shouldn't be nearly strong enough to do this (as I said, everything is very stable in MD without restraints), the rest of the simulation settings are very standard. I'm at a loss to explain what is going on, and this has thrown into question what I thought was >50ns of production run. Can anyone help?



NAMD version is 2.9-ibverbs
Using CHARMM-36 parameters
Explicit water, 0.15M sodium chloride
I've checked that the system is neutral

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