Hi Bill,
So TEMP is alright in starting nanoseconds but after 40ns TEMP have NaN.
-------------------------------------------------------
Amber 16 PMEMD 2016
-------------------------------------------------------| PMEMD implementation of SANDER, Release 16| Run on 10/18/2019 at 06:12:26| Executable path: pmemd.cuda
| Working directory: /newhome/vl18981/for_hira/MC/charmm/1
| Hostname: node46-007 [-O]verwriting outputFile Assignments:
| MDIN: ../md10.i
| MDOUT: md40.log
| INPCRD: md30.rst
| PARM: tem1-mem.parm7
| RESTRT: md40.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md40.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 549013 based on wallclock time in
microseconds.
.... Molecular dynamics:
nstlim = 5000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000Berendsen (weak-coupling) temperature regulation:
temp0 = 320.00000, tempi = 0.00000, tautp = 10.00000SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1| Energy averages sample interval:
| ene_avg_sampling = 500Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 75.500 Box Y = 75.500 Box Z = 75.500
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------Cpptraj Generated Restart
begin time read from input coords = 11460.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
DUMPFREQ 500 0 0.000000 0.000000 0 0
** No weight changes given ** RESTRAINTS:
Requested file redirections:
DISANG = rest.rst
DUMPAVE = rest.tra
Restraints will be read from file: rest.rst
Here are comments from the DISANG input file: Number of restraints read = 1 Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 13362 Sum of charges from parm topology file = 0.00000000
Forcing neutrality...| Dynamic Memory, Types Used:
| Reals 1257434
| Integers 1466799| Nonbonded Pairs Initial Allocation: 7392693| GPU memory information (estimate):
| KB of GPU memory in use: 97248
| KB of CPU memory in use: 48864--------------------------------------------------------------------------------
4. RESULTS
-------------------------------------------------------------------------------- ---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.47
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.89
|--------------------------------------------------- NSTEP = 500 TIME(PS) = 11461.000 TEMP(K) = 299.66 PRESS = 0.0
Etot = -119539.3132 EKtot = 26987.4043 EPtot = -146526.7175
BOND = 837.8134 ANGLE = 2119.4571 DIHED = 2533.3945
UB = 241.4004 IMP = 135.1555 CMAP = -102.6297
1-4 NB = 604.5422 1-4 EEL = 8704.1475 VDWAALS = 12039.2015
EELEC = -173639.1999 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
check COM velocity, temp: 0.000013 0.00(Removed) NSTEP = 1000 TIME(PS) = 11462.000 TEMP(K) = 299.30 PRESS = 0.0
Etot = -119355.9523 EKtot = 26955.0449 EPtot = -146310.9972
BOND = 821.2603 ANGLE = 2112.6416 DIHED = 2534.1208
UB = 247.3605 IMP = 135.4554 CMAP = -91.8790
1-4 NB = 636.8714 1-4 EEL = 8793.5624 VDWAALS = 11666.4034
EELEC = -173166.7940 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
=============================================================================== NSTEP = 1500 TIME(PS) = 11463.000 TEMP(K) = 299.84 PRESS = 0.0
Etot = -119172.6971 EKtot = 27004.0586 EPtot = -146176.7557
BOND = 827.6985 ANGLE = 2136.0365 DIHED = 2534.8472
UB = 244.8267 IMP = 137.2601 CMAP = -112.0989
1-4 NB = 626.2361 1-4 EEL = 8757.7227 VDWAALS = 11736.4103
EELEC = -173065.6950 EHBOND = 0.0000 RESTRAINT = 0.0000
But in further simulations, it gives NaN and then stops...
------------------------------------------------------------------------------
4. RESULTS
-------------------------------------------------------------------------------- ---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.47
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.89
|---------------------------------------------------
wrapping first mol.: NaN NaN NaN NSTEP = 500 TIME(PS) = 54961.000 TEMP(K) = NaN PRESS = 0.0
Etot = NaN EKtot = NaN EPtot = **************
BOND = 0.0000 ANGLE = 1623414.6174 DIHED = 0.0000
UB = 0.0000 IMP = 417024.3426 CMAP = 70.0043
1-4 NB = ************** 1-4 EEL = ************** VDWAALS = -1506.0876
EELEC = ************** EHBOND = 0.0000 RESTRAINT = **************
EAMBER (non-restraint) = **************
------------------------------------------------------------------------------ NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
check COM velocity, temp: NaN NaN(Removed)
wrapping first mol.: NaN NaN NaN NSTEP = 1000 TIME(PS) = 54962.000 TEMP(K) = NaN PRESS = 0.0
Etot = NaN EKtot = NaN EPtot = **************
BOND = 0.0000 ANGLE = 1623414.6174 DIHED = 0.0000
UB = 0.0000 IMP = 417024.3426 CMAP = 70.0043
1-4 NB = ************** 1-4 EEL = ************** VDWAALS = -1506.0876
EELEC = ************** EHBOND = 0.0000 RESTRAINT = **************
EAMBER (non-restraint) = **************
------------------------------------------------------------------------------ NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
wrapping first mol.: NaN NaN NaN NSTEP = 1500 TIME(PS) = 54963.000 TEMP(K) = NaN PRESS = 0.0
Etot = NaN EKtot = NaN EPtot = **************
BOND = 0.0000 ANGLE = 1623414.6174 DIHED = 0.0000
UB = 0.0000 IMP = 417024.3426 CMAP = 70.0043
1-4 NB = ************** 1-4 EEL = ************** VDWAALS = -1506.0876
EELEC = ************** EHBOND = 0.0000 RESTRAINT = **************
EAMBER (non-restraint) = **************
------------------------------------------------------------------------------ NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
Can you suggest, how to fix this error?
Thanks,Hira
On Monday, October 21, 2019, 02:18:10 PM GMT+1, Bill Ross <ross.cgl.ucsf.edu> wrote:
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
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Received on Mon Oct 21 2019 - 07:00:02 PDT
