OK, sounds suspicious.
Hopefully you have some of these already, but I suggest you prepare two run
inputs
* 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
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
Hi,
One simulation at each dump rate doesn't lead to a reliable conclusion that
the change in volume may be related to the dump rate, because if you run
replicates at each dump rate, they would not reproduce each other. If you
run such replicates and there is, or is not, a consistent trend, then
Hi Peter,
Thank you for the swift reply. Here are some details about your answers. I
hope the problem will appear more clear with them.
> Increase/decrease by how much? Is it converged?
The results completely diverge, that is the problem. The interactions we
are observing through the simulations
Hi Vivien,
My answers are inline
On 08-02-18 12:28, Vivien WALTER wrote:
> Dear all,
>
> We are experiencing a strange problem with all-atom simulations using
> Gromacs and Charmm force field, and we have trouble to sort it out.
>
> We are simulating a single-ring sugar and we observe
Dear all,
We are experiencing a strange problem with all-atom simulations using
Gromacs and Charmm force field, and we have trouble to sort it out.
We are simulating a single-ring sugar and we observe radically different
behaviors of the molecule as a function of the simulation dump rate.
