If its infinite VDW then that usually comes from atoms overlapping. chimera
will check for vdw clashes, you can then edit the conformation by hand in a
text editor or try loading it into xleap which has basic atom-editing. Now
that I think of it, xleap also has a very robust minimiser although it is
also very slow it does tend to produce structures that don't explode when
it (eventually) converges.
On Thu, 20 Jun 2019 at 17:00, 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
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>
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Received on Thu Jun 20 2019 - 08:30:02 PDT
