Dear Amber users,
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
All the above protocol working well for protein without metal ion and I am
not getting any vlimit error in the restart production run, after 5 ns.
Moreover, when I am using the same protocol and input file in
another cluster for metal ion bound protein, everything is fine and I have
done 50 ns MD simulation without any error.
I am not getting where is the problem, please help me to solve this.
Thanks
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Received on Wed Jul 19 2017 - 08:00:06 PDT
