[28-IX-2012]
Hi,
I am trying to run some TI calculation tests, in explicit water solvent (TIP3P model) with AMBER 11 for a glucose molecule (GLYCAM06 force field) for the alpha to beta anomer transformation (GLA and GLB residue names). The NVT equilibration includes a heating slope of 100ps. followed by 200ps. at 298 K, (all in the same simulation step). I am using lambdas from 0 to 1 in growing intervals of 0.1 and a refinement at the edges (0.01; 0.05; 0.95 and 0.99).
Shortly after I sumbitted the job, the system failed (all of the lambda values) according to SHAKE problems, giving the error message:
"Softcore potentials require ntf=1 because SHAKE constraints on some bonds might be removed"
(See output files for lambda 0.01 attached)
I am aware that SC potentials don't get on very well with SHAKE algorithm and I used the "noshakemask" keyword to UNSHAKE the residues that contain the atoms involved in the transformation in both V0 and V1 states. So, the only residues under SHAKE in my system were the water molecules (the solvent).
The AMBER11 manual says that "noshakemask" must be used to unshake residues (which I did) and AMBER12 manual says also that "just setting noshakemask might not be enough, since this flag does not affect the settle
routine that handles rigid waters". The tutorials A9 and A6 don't say so much about this and I did not find any answer in the amber list.
Is it possible to run TI calculations applying shake only to solvent molecules? Can anyone give a clue to solve this problem?
Thank you very much.
Kepa K.
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Received on Fri Sep 28 2012 - 10:30:03 PDT
