Hi Kepa,
Three point solvent molecules are identified in the prmtop (and by Leap too
maybe?). I believe that SETTLE and not SHAKE is used to constrain those
when ntc > 1 and jfastw = 0 (default). If you set jfastw = 4 then normal
SHAKE is used. I think you can only get away with ntf > 1 when all
bonds/angles/dihedrals are constrained (*i.e.* when not using noshakemask).
Regards,
Brian
On Fri, Sep 28, 2012 at 1:27 PM, Kepa K. Burusco <kekoburgo.yahoo.es> wrote:
> [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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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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Received on Fri Sep 28 2012 - 11:30:03 PDT
