Re: [AMBER] How to get the jac.restrt?

From: David A Case <>
Date: Tue, 11 Dec 2018 07:46:36 -0500

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


AMBER mailing list
Received on Tue Dec 11 2018 - 05:00:02 PST
Custom Search