Hello,
Related to this:
I understand that there is lots to do before a release, but it would be
great if this kind of change (changing the default format of restrt files
written by sander/pmemd) would be documented in a changelog.
This is important as behaviour between sander from AmberTools16 (etc.) and
previous versions has changed, when given the same input file.
For the OP and others reading this thread:
In the input file for sander/pmemd/pmemd.cuda, you can set the format of
the restrt file with ntxo.
See section 18.6.3. in the manual:
ntxo Format of the final coordinates, velocities, and box size (if
constant volume or pressure run) written to file "restrt".
= 1 Formatted (ASCII)
= 2 (default) NetCDF file (recommended, unless you have a workflow that
requires the formatted form.)
For manual writers/editors: The entry on ioutfm in this section is now
outdated:
"While not the default option, binary trajectory files have many
advantages: they are smaller, higher precision, much faster to read and
write, and able to accept a wider range of coordinate (or velocity) values
than formatted trajectory files."
I would suggest deleting "While not the default option, "
Thanks,
Marc
On 15 June 2016 at 16:32, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Also, keep in mind that you can get details (# atoms, time, etc) from
> a NetCDF restart file using the `ncdump` utility (included with all
> NetCDF distributions).
>
> -Dan
>
> On Tue, Jun 14, 2016 at 3:59 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > No syntax change - NetCDF formats will be automatically recognized.
> >
> > -Dan
> >
> > On Tue, Jun 14, 2016 at 3:49 PM, Neha Gandhi <n.gandhiau.gmail.com>
> wrote:
> >> 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
> >> _______________________________________________
> >> 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)
>
>
>
> --
> -------------------------
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 17 2016 - 03:30:02 PDT
