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

Mark Abraham mark.j.abraham at gmail.com
Thu Feb 8 15:58:25 CET 2018

OK, sounds suspicious.

Hopefully you have some of these already, but I suggest you prepare two run
* macromolecule in a T-coupling group and water in a T-coupling group
* macromolecule in a T-coupling group and water+sugar in a T-coupling group
and run each .tpr at the two different dump rates. I don't think the
flavour of T-coupling is relevant. Assuming the results reproduce your
observations, please open an issue at https://redmine.gromacs.org/ and
attach the two .tpr and four .log files e.g. in a tarball file.



On Thu, Feb 8, 2018 at 3:47 PM Vivien WALTER <walter.vivien at gmail.com>

> 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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