Thank you a lot for the tip!
I’ll try that as the simulation blows up from the beginning. I have the vlimit exceeded error message and both incredibly high temperature and total energy at the first step.
Moreover, by watching the trajectory I only see the solvent water molecules going away (and not much happens with the protein and the ligand themselves).
Ruth
> On 25 Sep 2015, at 17:24, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Fri, Sep 25, 2015 at 11:08 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
> wrote:
>
>> 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..).
>>
>
> It's a little complicated, but it can be done. sander identifies water
> molecules that need to be dispatched to SETTLE by atom and residue name.
> So if you change the residue names of the three waters you don't want to
> SETTLE to something different (maybe QMW for QM water), that should do it.
>
> You can either do this by hand in the prmtop file (look for the
> RESIDUE_LABEL section), or using ParmEd in a Python program.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Sep 25 2015 - 09:00:03 PDT
