Hi Peter,
Thanks for the reply, I know we spoke in length on this mater only just
recently. Many thanks for that.
I’ve taken the time step of collagen in vacu down to 0.0001 and I’ve
dropped the temp down to 280. I hope, running over 16 cores for two days
that this should relieve any tension in
As a note to Alex (and the rest of the list), the coarse-grained Martini
forcefield is usually run with timesteps between 20-40 fs. 15fs is
already rather low. I do agree that longer equilibration at low timestep
(5 or 10) might help.
Alternatively, Do you think a semiisotropic pressure coupling m
Alex and Mark, thanks for the information. I’ll drop dt down,
significantly, drop the temperature, and run it for a long time.
Thanks for the ideas.
Anthony
On 15/12/2016 21:54, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Alex" wrote:
>Mark is right, no two ways about it.
Mark is right, no two ways about it. For initial equilibration and
assessing preexisting structural strains try vacuum, _much_ smaller
timesteps and possibly low temperatures in vacuum, only then transfer to
solvent, etc. Algorithmically, LINCS requires convergence and you already
are using a prett
Hi,
If a simulation isn't stable with a small time step (as I think you are
saying) then moving to a larger time step is guaranteed to make that worse.
Try an even smaller time step, for a long time, and see what happens. Or
take a subset of your protein and see what happens. Or simulate in vacuo
Hi all,
I¹m hoping for some help. I¹m very sorry, this is a bit of a long one.
I¹ve been struggling for almost a month trying to run a CG representation
of our all-atom model of a collagen protein (3 polypeptide chains in a
protein). Our original AMBER all-atom model had been successful modelling
