Ok, I see.
David A Case <david.case.rutgers.edu> 于2018年12月11日周二 下午8:46写道：
> On Tue, Dec 11, 2018, 王茜茜 wrote:
>
> > Recently, I learned the pmemd.amoeba simulation using the JAC example
> >in /home/softwares/amber14/src/pmemd.amoeba/build_amoeba/examples/JAC. I
> >can successfully build the required files according to the tutorial.
> > BUT when submitting a task, in Run.amoeba_jac.pmemd (mpirun -np 8
> >/home/case/amber12/bin/pmemd.amoeba.MPI -O -i mdin -p jac.prmtop -c
> >jac.restrt -o jac_amoeba.pmemd.8.out), I can not obtain the restart file
> by
> >myself. Where does the jac.restrt come from or how to produce it using the
> >.prmtop and inpcrd?
>
> We no longer distribute pmemd.amoeba, and people's recollection about
> how it works in fading. I *think* (worth a test) that only the prmtop
> needs to be converted for amoeba: the restart file is unchanged, so you
> can use the inpcrd file created by tleap.
>
> To repeat an earlier note: since both Tinker and OpenMM support the
> Amoeba force field, and since those programs are under active
> development, we main suggest that people use one of them to run Amoeba
> simulations. You have to prepare the system in Tinker anyway, so why
> not run the simulation in Tinker as well? There is also a very active
> group to Amoeba experts using those codes who are available to answer
> questions.
>
> ....dac
>
>
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Received on Tue Dec 11 2018 - 06:30:02 PST
