this definitely shows that it's the initial structure and not Amber or
EMAP. Amber isn't great at repairing very bad quality structures.
it might be worth trying to increase NCYC and decrease DX0. these are
described in the manual.
On Thu, Jun 20, 2019 at 11:00 AM Paula Mihaljevic-Juric <
paula.mihaljevic-juric.polytechnique.edu> wrote:
> Dear Josh and Carlos,
>
> I prepared the files from scratch using parameters and topology files for
> Amber so I do not think this would be the issue.
>
> My initial structure has a lot of clashes and problems (5.34 angstrom
> resolution obtained through cryo-EM). What I want to do is structural
> refinement using SGLD.
>
> When I put ntpr=1 into my minimisation file the output is:
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> | Flags: MPI
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/19/19 Time = 12:38:04
> 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)
>
>
> | Memory Use Allocated
> | Real 11123744
> | Hollerith 384471
> | Integer 6802006
> | Max Pairs 1
> | nblistReal 0
> | nblist Int 0
> | Total 114976 kbytes
>
> | 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.
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
>
> default_name
>
> General flags:
> imin = 1, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 1, ntrx = 1, ntwr =
> 500
> iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> 0
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
> Potential function:
> ntf = 1, ntb = 0, igb = 1, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 14.00000, intdiel = 1.00000
> saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
> gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
> rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
> alpb = 0
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 500, ncyc = 250, ntmin = 1
> dx0 = 0.01000, drms = 0.00010
>
> | MPI Timing options:
> | profile_mpi = 0
> | INFO: Old style inpcrd file read
>
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> default_name
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 0
> | Atom division among processors:
> | 0 1138 2263 3388 4512 5626 6758 7883
> | 9012 10126 11262 12390 13515 14634 15766 16883
> | 18015 19131 20262 21382 22515 23627 24760 25877
> | 27011 28126 29253 30379 31500 32638 33765 34884
> | 36021 37130 38253 39391 40500 41644 42750 43889
> | 45006 46127 47256 48386 49511 50626 51766 52877
> | 54021 55126 56264 57382 58506 59633 60759 61890
> | 63024 64148 65260 66395 67500 68646 69781 70884
> | 72012 73142 74281 75406 76505 77632 78777 79906
> | 81015 82133 83259 84398 85524 86627 87777 88899
> | 90015 91153 92273 93398 94531 95648 96774 97877
> | 99011 100131 101278 102393 103523 104648 105756 106883
> | 108015 109144 110271 111377 112504 113628 114763 115880
> | 117016 118131 119258 120389 121517 122625 123755 124889
> | 126102
> | Running AMBER/MPI version on 112 nodes
>
> | WARNING: The number of processors is not a power of 2
> | this may be inefficient on some systems.
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 5.0039E+14 N 7
>
> BOND = 316795.8041 ANGLE = 79730.4307 DIHED =
> 78396.3433
> VDWAALS = ************* EEL = -130977.6359 EGB =
> NaN
> 1-4 VDW = ************* 1-4 EEL = -23812.8259 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 5 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 6 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 7 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 8 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 9 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10 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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 11 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
>
>
>
> > On 20 Jun 2019, at 16:28, Josh Berryman <
> the.real.josh.berryman.gmail.com> wrote:
> >
> > 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
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
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> >>
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Received on Thu Jun 20 2019 - 08:30:03 PDT
