Dear Josh,
I do not have chimera. Do you suggest I use Xleap? How can I do it in Xleap, if you can perhaps briefly explain it?
Also, in terms of performance, do you know if pmemd.MPI will be faster than CHARMM?
Thank you so much for your help
> On 20 Jun 2019, at 17:16, Josh Berryman <the.real.josh.berryman.gmail.com> wrote:
>
> 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
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Received on Thu Jun 20 2019 - 08:30:03 PDT
