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 - 07:30:05 PDT
