On Fri, Sep 25, 2015 at 9:46 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:
> Dear Amber users,
>
> I’m running a molecular dynamics simulation of a protein with its ligand
> (which has three phosphates), a Mg+2 ion and three water molecules.
>
> After successfully minimising the structure quantum mechanically
> (RMS=2.25E-02 and GMAX=6.75E-01) and “heating” the explicit solvent as in
> tutorial B1, I run the molecular dynamics treating a few residues, the Mg
> ion and the three water molecules quantum mechanically, like during the
> minimisation.
>
> As I‘m looking for a reaction to proceed in the QM region, I remove the
> shake options from it with a noshakemask and, as the three water molecules
> are involved in this reaction, I also add jfastw=4, as advised in the
> manual in order to effectively remove the shake options from water
> molecules.
>
> Here is the input file:
>
> Constant Temp 300K MD
> &cntrl
> imin=0,
> irest=1, ntx=7,
> ntb=2, pres0=1.0, ntp=1, taup=1.0,
> cut=12.0,
> tempi=300.0, temp0=300.0,
> ntt=3, gamma_ln=2.0,
> nstlim=50000, dt=0.0005,
> ntpr=100, ntwx=10, ntwr=1000,
> ntc=2, ntf=2, jfastw=4,
> noshakemask = '.900-909,917-933,2645,2646-2689,2828-2851,2931-2939',
> ntr=1,
> restraintmask = ':170,185,@CA,C,N',
> restraint_wt=5.0,
> ifqnt=1,
> /
> &qmmm
> qmmask=':59,61,168,169,186-188',
> qmcharge=-2,
> qm_theory='PM3',
> qmshake=0,
> qmcut=12.0,
> /
>
> I guess that because of the thousands of water molecules present in the
> system, I get the error message “vlimit exceeded” from the first step..
See if you can isolate where the simulation is beginning to blow up by
printing out snapshots and energies every step for the first 100 steps or
so.
> So I wonder, is there any way to remove the shake options from the three
> water molecules in the QM region only and keep them in the rest of the
> solvent?
>
jfastw does not turn off the constraints on the water, it just solves them
using SHAKE instead of SETTLE (the latter is a faster, analytical solution
to a set of 3 distance constraints).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 25 2015 - 07:30:03 PDT
