On Wed, Jul 19, 2017, sangita kachhap wrote:
>
> I am studying metalloprotein using MD simulation and for this, I have used
> metal ion modeling tutorial of AMBER.
> I am doing minimization of metal ion bound protein in two steps-1st with
> restraint and 2nd without restraint, heating at NVT with restraint,
> releasing restraint in three steps, equilibration at NPT and the production
> run at NVT. Till production run of 5 ns, everything is fine but when
> restarting production after 5 ns getting following error.
>
> vlimit exceeded for step 0; vmax = **********
>
> Coordinate resetting cannot be accomplished,
> deviation is too large
> iter_cnt, my_bond_idx, i and j are : 2 22 6893 6894
This sounds like something is wrong with the restart file. Double/triple
check that you didn't just have a wrong file name, or that you are really
restarting from the exact file you finished with in the early step in the run
You can create a PDB file from the restart file, and look at the geometry
around atoms 6893 and 6894, which presumably are far from their idea geometry.
It doesn't look like this has anything to do with the presence or absence
of metal ions.
....dac
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Received on Wed Jul 19 2017 - 09:00:03 PDT
