Dear All,
(hope this message can be put under the original thread)
I solved this problem. The reason is, I was trying to fill the system with
water then minimise it, which is not good.
The better way is, prepare a waterbox that is even larger than the system box.
Then minimise that water
Hello Cheng,
The lines at the end of this mail are the extra parameters we usually
define in our lab whenever we need to use soft potentials.
They are based on the parameters given by CHARMM-GUI for the Martini
Maker. However, you *may* need to make alterations if there are
conflicts with
Dear Fotis and Peter,
Thank you very much for the help.
Fotis, Can I modify the mdp file to use "soft" potential modifier, how to do
that?
I think my problem is not the first reason (i.e. something wrong with the
system structure or topology), because the potential is decreasing for the
Hi all,
@Fotis, the softcore potential for minimization sounds interesting, I'll
remember that!
Alternatively, something we also occasionally do in the lab, is replace
all constraints for stiff bonds during minimization and if needed the
first bit of equilibration.
Peter
On 22-01-19 13:24,
Hello all,
I would like to point out step 2 of the original poster's message:
/2) Then 10 of this protein were inserted to a box, followed by a />>/minimization. It "stopped
because the algorithm tried to make a new step />>/whose size was too small, or there was no change
in the energy
Hi,
You can reduce the timestep during equilibrations to e.g. 10 fs, or 5
when you have a really bad starting configuration. Bring it back up to
20 (in steps if needed) before starting your actual
equilibration/production though.
In addition, you can raise the lincs_order to 8.
And yes, the
Hi,
I don't have any experience of coarse-grained systems, but everything looks
OK from this level. It is normal to troubleshoot by visualizing your input
and progress result. Minimizers are local, so if you start from something
that has a frustration that can't be resolved, you are stuck.
I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to
100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100",
i.e. outputting dozens of pdb files before the "LINCS warnings".
Then I looked at the edr files.
The potential in "emtol = 1000" and
I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told
"Too many LINCS warnings" in the minimization after solvation with
coarse-grained waters.
I try to diagnose the problems based on
http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up
