[gmx-users] Problem with Gromacs and Charmm force field dump rates

[Vivien WALTER]

Hi Mark,

Thank you for the swift reply.

Sorry for not being clear enough. As I tried to explain in my previous
mail, the problem comes from the behavior of the sugar molecules regarding
the macromolecule, not just from the box size (which I only used as an
example on the first mail to explain we had a divergence in the results).

At high dump rates, the saccharide adsorbs on the macromolecule, while at
low dump rates the saccharide desorbs from it.
We ran several tests to try to understand the problem further. Here is one
example : if I take the resulting system of the high dump rate simulation
(sugar adsorbed) and restart from this configuration with the same high
dump rate, the sugar stays adsorbed. This behavior was confirmed on several
restart.
If I take the same system (high dump rate / sugar adsorbed) and this time
change the dump rate to the low one, the sugar will desorb from it during
the first simulation. And I can restart it, still with the low dump rate,
the sugar will not adsorb back.

This trend in the saccharide-macromolecule interactions was observed on
several systems with different number of saccharide molecules in the box,
but also at different temperatures. And it's always the same: at high dump
rate, the sugar adsorbs, but desorbs at low dump rate.

I hope the problem is more clear now.

Best regards,
Vivien

-- 
Dr. Vivien WALTER
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