Hi,
I am trying to run MD simulation in implicit solvent.
In the initial nanoseconds, results are fine but after 90 nanoseconds I get an error of NaNs in coordinates and the simulation stops.
Here is the output file:
-------------------------------------------------------
Amber 16 PMEMD 2016
-------------------------------------------------------| PMEMD implementation of SANDER, Release 16| Run on 10/19/2019 at 08:57:45| Executable path: pmemd.cuda
| Working directory: /newhome/vl18981/for_hira/MC/charmm/1
| Hostname: node46-007 [-O]verwriting outputFile Assignments:
| MDIN: ../md10.i
| MDOUT: md90.log
| INPCRD: md80.rst
| PARM: tem1-mem.parm7
| RESTRT: md90.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md90.nc
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:10ns NVT MD production (weak coupling of 10 ps)
&cntrl
imin=0, irest=1, ntx=5, iwrap=1,
nstlim=5000000, dt=0.002,
ntpr=500, ntwx=500, ioutfm=1, ntwr=50000,
ntc=2, ntf=2, cut=8.0,
ntb=1, ntp=0,
ntt=1, tautp=10.0, temp0=320.0
nmropt=1,
/
&wt type='DUMPFREQ', istep1=500 /
&wt type='END' /
DISANG=rest.rst
DUMPAVE=rest.tra
/
Note: ig = -1. Setting random seed to 664041 based on wallclock time in
microseconds.|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 16.0.0
|
| 02/25/2016
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| Precision model in use:|--------------------------------------------------------|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184 pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: 0
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla K20m
| CUDA Device Global Mem Size: 4799 MB
| CUDA Device Num Multiprocessors: 13
| CUDA Device Core Freq: 0.71 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL| Largest sphere to fit in unit cell has radius = 37.724| New format PARM file being parsed.
| Version = 1.000 Date = 09/09/19 Time = 12:57:23
| Force field information read from topology file:
| >>>> CHARMM36 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
| CHARMM: >>>>>>>>>>>> All-hydrogen parameters used in the <<<<<<<<<<<<<<<<
|
|CHARMM: CHARMM force field in use.
|
|CHARMM: CHARMM force field in use.| 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: Off Diagonal (NBFIX) LJ terms found in prmtop file.
| The prmtop file has been modified to support atom
| type based pairwise Lennard-Jones terms.
| Duplicated 0 dihedrals| Duplicated 0 dihedrals--------------------------------------------------------------------------------
1. RESOURCE USE:
-------------------------------------------------------------------------------- getting new box info from bottom of inpcrd
NATOM = 44261 NTYPES = 61 NBONH = 42138 MBONA = 2076
NTHETH = 18031 MTHETA = 2819 NPHIH = 7773 MPHIA = 5142
NHPARM = 0 NPARM = 0 NNB = 76127 NRES = 13707
NBONA = 2076 NTHETA = 2819 NPHIA = 5142 NUMBND = 106
NUMANG = 234 NPTRA = 495 NATYP = 1 NPHB = 0
IFBOX = 1 NMXRS = 51 IFCAP = 0 NEXTRA = 0
NCOPY = 0|CHARMM: Reticulating splines.| ERROR: NaN(s) found in input coordinates.
This likely means that something went wrong in the previous simulation.
The output file of md80.log is alright but .rst file has NaNs. While the previous files (md70.log md70.nc, and md70.rst) are alright.
Can you please suggest what is wrong?
Thanks,Hira
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Received on Mon Oct 21 2019 - 06:30:04 PDT
