I would start by turning off the emap.
On Thu, Jun 20, 2019, 10:09 AM Paula Mihaljevic-Juric <
paula.mihaljevic-juric.polytechnique.edu> wrote:
> All the calculations were performed on CPUs. I tested the script on my
> desktop machine on 16 CPUs and the simulation was running on both sander
> and pmemd (although it still had NaN in both cases, but it did not crash).
> When I was trying to run it on 112 cores on the supercomputer, only
> sander.MPI is working and for pmemd.MPI I get " NaN(s) found in the input
> coordinates” error and the simulation stops.
>
> My system is composed of ~ 127k atoms. I am using GB_HCT and I am using
> map constraints. I briefly minimised the structure as well where I have
> obtained notification: RESTARTED DUE TO LINMIN FAILURE, but I read that
> this error is not really an error.
>
> Technically, I just want to test performance of AMBER when using EMAP,
> because I would like to use SGLD which is also implemented in CHARMM and
> rather too slow. I am not sure whether it will be faster than CHARMM when
> using pmemd.MPI.
>
> I do not have any non-standard parameters. It is highly possible that I am
> missing something in my script.
>
> This is my input file:
>
>
> &cntrl
> imin=0, ntb=0,
> igb=1, ntpr=500, ntwx=500,
> ntt=3, gamma_ln=1.0,
> tempi=50.0, temp0=300.0,
> nstlim=500, dt=0.002,
> ntc=1
> cut=14.0,
> /
> &emap
> mapfile='./EMAP/emd_8149.map',
> atmask=':*&!.H=',
> fcons=0.5,
> move=1,
> ifit=1,
> mapfit='EMAP/emd_1.map',
> molfit='pdb/emd_1.pdb', /
>
> Thank you
> Paula
>
>
> > On 20 Jun 2019, at 15:52, Carlos Simmerling <carlos.simmerling.gmail.com>
> wrote:
> >
> > Can you tell us more about what you're simulating? Any nonstandard
> > parameters? For implicit solvent, which model and which radii set?
> >
> > NaN is bad regardless of whether the simulation stops or not. When you
> say
> > sander. MPI and pmemd.MPI work, which code did not work? Was it on cpu or
> > gpu?
> >
> > On Thu, Jun 20, 2019, 9:35 AM Paula Mihaljevic-Juric <
> > paula.mihaljevic-juric.polytechnique.edu> wrote:
> >
> >> Hi!
> >>
> >> I am trying to run MD simulation in implicit solvent.
> >>
> >> I have tested the script on my desktop computer where for some results I
> >> would obtain NaN, but the simulations would not stop. Both sander.MPI
> and
> >> pmemd.MPI worked fine.
> >>
> >> However, when I am trying to use the same script on a supercomputer, the
> >> simulation crashes with the error NaN(s) found in the input coordinates
> >> while using pmemd.MPI. The simulation does not crash when using
> sander.MPI.
> >>
> >> What am I doing wrong? How can I fix this?
> >>
> >> Thanks
> >>
> >> Paula
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Received on Thu Jun 20 2019 - 07:30:04 PDT
