The default restart format has changed in Amber 16 to NetCDF restart,
which is an overall better format than the old ASCII format. If you
need an ASCII version of your restart you can use cpptraj to create
one like so:
cpptraj -p solvated.prmtop -y heat.rst -x heat.ascii.rst7
-Dan
On Tue, Jun 14, 2016 at 3:29 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Dear List,
>
> I installed AMBER16 recently and compiled the cuda version both parallel
> and serial.
>
> The .out log files look complete but it seems the .rst file has issues
> (AMBER16). I think it is in binary format ..there are no coordinates
> written to it but the size of the file seems correct. I tried compiling
> twice and it didn't give any errors.
>
> Upon running the same with AMBER14, it outputs coordinates in the right
> format in the .rst file.
>
> Here is the output file with AMBER16
>
> | PMEMD implementation of SANDER, Release 16
>
> | Run on 06/15/2016 at 07:07:25
>
> | Executable path: /home/gandhin/amber16/bin/pmemd.cuda.MPI
> | Working directory: /home/gandhin/caroline/pep4
> | Hostname: cl2n002
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: heat.in
>
> | MDOUT:
> heat.out
> | INPCRD:
> sys_min.rst
> | PARM:
> solvated.prmtop
> | RESTRT:
> heat.rst
> | REFC:
> sys_min.rst
> | MDVEL:
> mdvel
> | MDEN:
> mden
> | MDCRD:
> mdcrd
> | MDINFO:
> mdinfo
> |LOGFILE:
> logfile
> | MDFRC:
> mdfrc
>
>
> Here is the input file:
>
> Heating
> System
> &cntrl
>
> imin=0,
> nmropt=1,
> ntx=1,
> irest=0,
> ntpr=500, ntwr=500, ntwx=500,
> iwrap=1,
> ntf=2, ntb=1, cut=12.0,
> nsnb=20,
>
> igb=0,
> ibelly=0,
> ntr=1,
> nstlim=250000, nscm=500,
> dt=0.002,
> ntt=1, temp0=0.0, tempi=0.0,
> tautp=0.5
>
> ntc=2,restraintmask=':1-20',
>
> restraint_wt=10.0,
> &end
>
>
>
> &wt type='REST', istep1=0, istep2=0, value1=1.0, value2=1.0,
> &end
> &wt type='TEMP0', istep1=0, istep2=250000, value1=0.0, value2=293,
> &end
> &wt type='END'
> &end
>
>
> Note: ig = -1. Setting random seed to 545793 based on wallclock time in
> microseconds and disabling the synchronization of random numbers
> between tasks to improve performance.
> | INFO: The nsnb ctrl option does not affect nonbonded list update
> frequency.
> | It does affect steepest descent minimization freq if ntmin == 0
>
> |--------------------- 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:
> | [SPFP] - Single Precision Forces, 64-bit Fixed Point
> | Accumulation. (Default)
> |
> |--------------------------------------------------------
>
> |----------------- 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 --------------------
> |
> | Task ID: 0
> | CUDA_VISIBLE_DEVICES: 0,1
> | CUDA Capable Devices Detected: 2
> | CUDA Device ID in use: 0
> | CUDA Device Name: Tesla M2090
> | CUDA Device Global Mem Size: 5375 MB
> | CUDA Device Num Multiprocessors: 16
> | CUDA Device Core Freq: 1.30 GHz
> |
> |
> | Task ID: 1
> | CUDA_VISIBLE_DEVICES: 0,1
> | CUDA Capable Devices Detected: 2
> | CUDA Device ID in use: 1
> | CUDA Device Name: Tesla M2090
> | CUDA Device Global Mem Size: 5375 MB
> | CUDA Device Num Multiprocessors: 16
> | CUDA Device Core Freq: 1.30 GHz
> |
> |--------------------------------------------------------
>
> |---------------- GPU PEER TO PEER INFO -----------------
> |
> | Peer to Peer support: DISABLED
> |
> | (Selected GPUs cannot communicate over P2P)
> |
> |--------------------------------------------------------
>
>
> | Conditional Compilation Defines Used:
> | MPI
> | PUBFFT
> | BINTRAJ
> | CUDA
> | EMIL
>
> | Largest sphere to fit in unit cell has radius = 36.851
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/29/16 Time = 14:56:38
>
> | 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 new box info from bottom of inpcrd
> NATOM = 39632 NTYPES = 20 NBONH = 39470 MBONA = 152
> NTHETH = 330 MTHETA = 209 NPHIH = 671 MPHIA = 637
> NHPARM = 0 NPARM = 0 NNB = 54069 NRES = 13141
> NBONA = 152 NTHETA = 209 NPHIA = 637 NUMBND = 56
> NUMANG = 122 NPTRA = 125 NATYP = 34 NPHB = 1
> IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> | Coordinate Index Table dimensions: 10 10 10
> | Direct force subcell size = 7.3739 7.3897 7.3701
>
> BOX TYPE: RECTILINEAR
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
> --------------------------------------------------------------------------------
>
> default_name
>
>
> General flags:
> imin = 0, nmropt = 1
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 2, ntpr = 500, ntrx = 1, ntwr =
> 500
> iwrap = 1, ntwx = 500, ntwv = 0, ntwe
> = 0
> ioutfm = 1, ntwprt = 0, idecomp = 0,
> rbornstat= 0
>
> Potential function:
> ntf = 2, ntb = 1, igb = 0, nsnb
> = 20
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
> restraint_wt = 10.00000
>
> Molecular dynamics:
> nstlim = 250000, nscm = 0, nrespa = 1
> t = 0.00000, dt = 0.00200, vlimit = -1.00000
>
> Berendsen (weak-coupling) temperature regulation:
> temp0 = 0.00000, tempi = 0.00000, tautp = 0.50000
>
> SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
>
> NMR 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 = 500
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme
> = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 73.739 Box Y = 73.897 Box Z = 73.701
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
> Cutoff= 12.000 Tol =0.100E-04
> Ewald Coefficient = 0.22664
> Interpolation order = 4
>
> | PMEMD ewald parallel performance parameters:
> | block_fft = 0
> | fft_blk_y_divisor = 2
> | excl_recip = 0
> | excl_master = 0
> | atm_redist_freq = 320
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> default_name
>
> Mask :1-20; matches 295 atoms
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
> default_name
>
> begin time read from input coords = 0.000 ps
>
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> REST 0 0 1.000000 1.000000 0 0
> TEMP0 0 250000 0.000000 293.000000 0 0
>
> RESTRAINTS:
> ** No restraint defined **
>
> Done reading weight changes/NMR restraints
>
>
>
> Number of triangulated 3-point waters found: 13108
>
> Sum of charges from parm topology file = -0.00000002
> Forcing neutrality...
>
> | Dynamic Memory, Types Used:
> | Reals 1820586
> | Integers 1441862
>
> | Nonbonded Pairs Initial Allocation: 12293846
>
> | GPU memory information (estimate):
> | KB of GPU memory in use: 85032
> | KB of CPU memory in use: 56682
>
> | Running AMBER/MPI version on 2 nodes
>
>
>
>
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Jun 14 2016 - 15:00:02 PDT
