Hi,
My initial thought is that perhaps your system is not yet
well-equilibrated enough for production dynamics. Remember that the
tutorials should be treated as examples or guidelines of how to do
something. They do not necessarily represent a generally applicable
procedure (in fact, there is a warning in red in that lipid tutorial
you linked to that refers to this). You can't just plug in any system
to a tutorial and expect things to just work - you have to understand
what's going on "under the hood" as well.
I recommend some analysis of your coordinates prior to the production
step. Look at the density, area per lipid, etc, and make sure that
these look like they are converging to reasonable values for your
system. If you think your system is equilibrated, try a shorter run
(nstlim=5000) and print out the energies more often (ntpr=1 to 10 or
so) to get a better idea for what may be going on.
Hope this helps,
-Dan
On Tue, Mar 15, 2016 at 6:51 AM, Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> 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
> ------------------------------------------------------------------------------
>
>
> <https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
>
>
> <https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 15 2016 - 08:00:05 PDT
