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
>>>>>> _______________________________________________
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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>> _______________________________________________
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Received on Thu Jun 20 2019 - 08:30:02 PDT
