Re: [AMBER] jfastw=4 and vlimit exceeded

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 25 Sep 2015 10:27:43 -0400

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
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