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
Received on Wed Jun 15 2016 - 09:00:13 PDT
