Hello Jason,
Thank you a lot for the answer, I’ll check it carefully.
If I understand well then, with the input file I’m using, the three water molecules in the QM region aren’t constrained: nor by shake (because of the noshakemask) neither by settle (because of jfastw=4) and the rest of the water molecules are constrained using shake, is that right?
If so, is there any way to remove the constrains using settle from the three water molecules in the QM region only? Because when I run the same molecular dynamics simulation without jfastw=4 I don’t have this problem (even though the run is not over yet..).
> On 25 Sep 2015, at 16:27, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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 - 08:30:05 PDT
