Dear Amber List experts,
I have followed all protocols from TUTORIAL A16: An Amber Lipid Force Field Tutorial: Lipid14<http://ambermd.org/tutorials/advanced/tutorial16/index.html>
for MD simulation and files preparing of my protein in membrane.
I have successfully passed all steps but the last productive MD.
I have used prod.in file that is a copy of the original 05_Prod.in<
http://ambermd.org/tutorials/advanced/tutorial16/include/05_Prod.in> script in the command:
nohup pmemd.cuda -O -i prod.in<
http://prod.in> -o prod1.out -p ../*.prmtop \
-c ../4_/hold10.rst -r prod1.rst -x prod1.nc<
http://prod1.nc> &
Examining the MD output file I have observed an error message:
Attempting MC barostat change: Failed
Please find below a fragment of the output file with all details
including the text of the used prod.in file.
Please advise me what changes in the prod.in parameters
should be used to resolve the problem.
Thank you,
Michael
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 14
| Run on 03/15/2016 at 13:47:45
| Executable path: pmemd.cuda
| Working directory: /home/shokhen/Documents/5f5b/5_
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: prod.in
| MDOUT: prod1.out
| INPCRD: ../4_/hold10.rst
| PARM: ../mc.prmtop
| RESTRT: prod1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: prod1.nc
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:
Protein Lipid production 310K 125ns
&cntrl
imin=0,
ntx=5,
irest=1,
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=62500000,
ntt=3,
gamma_ln=1.0,
temp0=303.0,
ntpr=5000,
ntwr=500000,
ntwx=5000,
dt=0.002,
ig=-1,
ntb=2,
ntp=2,
cut=10.0,
ioutfm=1,
ntxo=2,
barostat=2,
/
Note: ig = -1. Setting random seed to 703795 based on wallclock time in
microseconds.
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 14.0.1
|
| 06/20/2014
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX TITAN
| CUDA Device Global Mem Size: 6143 MB
| CUDA Device Num Multiprocessors: 14
| CUDA Device Core Freq: 0.88 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 34.888
| New format PARM file being parsed.
| Version = 1.000 Date = 03/14/16 Time = 13:03:58
| 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
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting box info from netcdf restart file
NATOM = 48860 NTYPES = 24 NBONH = 39447 MBONA = 9250
NTHETH = 33060 MTHETA = 10615 NPHIH = 53704 MPHIA = 35939
NHPARM = 0 NPARM = 0 NNB = 162244 NRES = 9308
NBONA = 9250 NTHETA = 10615 NPHIA = 35939 NUMBND = 88
NUMANG = 194 NPTRA = 253 NATYP = 53 NPHB = 1
IFBOX = 1 NMXRS = 50 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 14 12 15
| Direct force subcell size = 5.5488 5.8147 5.8347
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 5000, ntrx = 1, ntwr = 500000
iwrap = 0, ntwx = 5000, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 62500000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 703795
temp0 = 303.00000, tempi = 0.00000, gamma_ln= 1.00000
Pressure regulation:
ntp = 2
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
Monte-Carlo Barostat:
mcbarint = 100
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 5000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 77.683 Box Y = 69.776 Box Z = 87.521
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 80 NFFT2 = 72 NFFT3 = 96
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 5420.000 ps
Number of triangulated 3-point waters found: 8585
Sum of charges from parm topology file = -0.00048135
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 1953878
| Integers 3235415
| Nonbonded Pairs Initial Allocation: 14778928
| GPU memory information (estimate):
| KB of GPU memory in use: 327439
| KB of CPU memory in use: 69715
--------------------------------------------------------------------------------
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 = 0.8314E-11 at 2.736960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.33
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.80
|---------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
NSTEP = 5000 TIME(PS) = 5430.000 TEMP(K) = 302.62 PRESS = 0.0
Etot = -76479.2165 EKtot = 32212.5273 EPtot = -108691.7438
BOND = 3129.9050 ANGLE = 12010.4285 DIHED = 8922.3943
1-4 NB = 3003.3686 1-4 EEL = 19841.7423 VDWAALS = 2219.1152
EELEC = -157818.6978 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 473431.6153
Density = 1.0263
------------------------------------------------------------------------------
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Received on Tue Mar 15 2016 - 06:00:03 PDT
