Try running parmed on your top file and using it to examine atomic radii
etc. If you imported from a charmm format then maybe that didn't work as
well as it seemed to.
Josh Berryman
On Thu, 20 Jun 2019 at 16:21, Paula Mihaljevic-Juric <
paula.mihaljevic-juric.polytechnique.edu> wrote:
> Dear Carlos,
>
> I have already tried and I obtain the same error.
>
> This was my minimisation input:
>
> Initital minimisation prior to MD GB model
> &cntrl
> imin=1,
> maxcyc=500,
> ncyc=250,
> ntb=0,
> igb=1,
> cut=14
> ntc=1
> /
>
> This was the output:
>
> BOND = NaN ANGLE = NaN DIHED =
> NaN
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -2295502.5997
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> 0.0000
>
> ... RESTARTED DUE TO LINMIN FAILURE ...
>
> ... RESTARTED DUE TO LINMIN FAILURE ...
>
> ... RESTARTED DUE TO LINMIN FAILURE ...
>
> ... RESTARTED DUE TO LINMIN FAILURE ...
>
> ... RESTARTED DUE TO LINMIN FAILURE ...
>
> ***** REPEATED LINMIN FAILURE *****
>
> ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO
> *****
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 271 NaN NaN 0.0000E+00 HH31 1
>
> BOND = NaN ANGLE = NaN DIHED =
> NaN
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -2295502.5997
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> 0.0000
>
>
> --------------------------------------------------------------------------------
> 5. TIMINGS
>
> --------------------------------------------------------------------------------
>
> | Read coords time 0.14 ( 0.04% of Total)
> | Calc gb radii 59.39 (19.31% of Gen B)
>
>
> This is the output of the md simulation:
>
>
>
> | Conditional Compilation Defines Used:
> | MPI
> | FFTW_FFT
> | BINTRAJ
> | MKL
> | EMIL
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/19/19 Time = 12:38:04
>
> | Note: 1-4 EEL scale factors are being read from the topology file.
>
> | Note: 1-4 VDW scale factors are being read from the topology file.
> | INFO: Reading atomic numbers from topology file.
> | Duplicated 0 dihedrals
>
> | Duplicated 0 dihedrals
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> NATOM = 126102 NTYPES = 12 NBONH = 55481 MBONA = 75305
> NTHETH = 126750 MTHETA = 109484 NPHIH = 236468 MPHIA = 265051
> NHPARM = 0 NPARM = 0 NNB = 701025 NRES = 6163
> NBONA = 75305 NTHETA = 109484 NPHIA = 265051 NUMBND = 117
> NUMANG = 287 NPTRA = 257 NATYP = 47 NPHB = 0
> IFBOX = 0 NMXRS = 34 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> Implicit solvent radii are modified Bondi radii (mbondi)
> | ERROR: NaN(s) found in input coordinates.
> This likely means that something went wrong in the previous
> simulation.
>
>
>
> > On 20 Jun 2019, at 16:15, Carlos Simmerling <carlos.simmerling.gmail.com>
> wrote:
> >
> > 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
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
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> >>
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>
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Received on Thu Jun 20 2019 - 07:30:06 PDT
