Thanks Daniel for quick reply.
Has the syntax changed to read the restart files from previous run or I can
still use -c to read netcdf restart?
-Neha
On 15 June 2016 at 07:34, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Tue Jun 14 2016 - 15:00:03 PDT
