Have you looked at e.g. TEMP in the mdout file?
Bill
On 10/21/19 6:13 AM, Hira Jabeen wrote:
> 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
> _______________________________________________
> 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
Received on Mon Oct 21 2019 - 06:30:05 PDT
