[AMBER] PMEMD in amber12

From: Mary Varughese <maryvj1985.gmail.com>
Date: Thu, 14 Mar 2013 20:34:05 +0530

Sir,

We have installed amber12 in a GPU server. Test run fine.
On trying pmemd.cuda.MPI on a protein-ligand system. Its hanging on the
last line of the .out file i attached together. After half an hour (but
without showing any error) i terminated the run. the same with a dna-
ligand system. Please have a look at the .out file which includes all the
inputs given. And i am trying pmemd for the first time. Please give some
suggestions too.
"
The same .out file is given below:

-------------------------------------------------------

Amber 11 SANDER 2010

-------------------------------------------------------

| PMEMD implementation of SANDER, Release 11

| Run on 03/14/2013 at 19:54:49

[-O]verwriting output

File Assignments:

| MDIN: TbNrb_md9.in

| MDOUT: TbNrb_md9.out

| INPCRD: TbNrb_md8.rst

| PARM: TbNrb.prmtop

| RESTRT: TbNrb_md9.rst

| REFC: refc

| MDVEL: mdvel

| MDEN: mden

| MDCRD: TbNrb_md9.mdcrd

| MDINFO: mdinfo

|LOGFILE: logfile

 Here is the input file:

 Tb-Ntr complex : 200ps MD (production run in NPT)

&cntrl

imin = 0,

irest = 1,

ntx = 5,

ntb = 2, ntp = 1, pres0 = 1.0,

cut = 10,

ntr = 0,

ntc = 2,

ntf = 2,

tempi = 300.0,

temp0 = 300.0,

ntt = 3,

gamma_ln = 1,

nstlim = 1000, dt = 0.002,

ntpr = 500, ntwx = 500, ntwr = 1000,

/


|--------------------- INFORMATION ----------------------

| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.

| Version 12.0

|

| 03/19/2012

|

| Implementation by:

| Ross C. Walker (SDSC)

| Scott Le Grand (nVIDIA)

| Duncan Poole (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:

| [SPDP] - Hybrid Single/Double Precision (Default).

|

|--------------------------------------------------------

 |------------------- GPU DEVICE INFO --------------------

|

| Task ID: 0

| CUDA Capable Devices Detected: 1

| 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 Capable Devices Detected: 1

| 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: 2

| CUDA Capable Devices Detected: 1

| 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: 3

| CUDA Capable Devices Detected: 1

| 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: 4

| CUDA Capable Devices Detected: 1

| 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: 5

| CUDA Capable Devices Detected: 1

| 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: 6

| CUDA Capable Devices Detected: 1

| 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: 7

| CUDA Capable Devices Detected: 1

| 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

|

|--------------------------------------------------------

  | Conditional Compilation Defines Used:

| DIRFRC_COMTRANS

| DIRFRC_EFS

| DIRFRC_NOVEC

| MPI

| PUBFFT

| FFTLOADBAL_2PROC

| BINTRAJ

| CUDA

 | Largest sphere to fit in unit cell has radius = 47.238

| New format PARM file being parsed.

| Version = 1.000 Date = 10/04/12 Time = 11:18:48

| 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 = 119092 NTYPES = 20 NBONH = 112233 MBONA = 6978

NTHETH = 14955 MTHETA = 9471 NPHIH = 29675 MPHIA = 23498

NHPARM = 0 NPARM = 0 NNB = 214731 NRES = 36118

NBONA = 6978 NTHETA = 9471 NPHIA = 23498 NUMBND = 78

NUMANG = 158 NPTRA = 71 NATYP = 52 NPHB = 1

IFBOX = 2 NMXRS = 44 IFCAP = 0 NEXTRA = 0

NCOPY = 0

| Coordinate Index Table dimensions: 17 17 17

| Direct force subcell size = 6.8064 6.8064 6.8064

BOX TYPE: TRUNCATED OCTAHEDRON

--------------------------------------------------------------------------------

2. CONTROL DATA FOR THE RUN

--------------------------------------------------------------------------------

 General flags:

imin = 0, nmropt = 0

Nature and format of input:

ntx = 5, irest = 1, ntrx = 1

Nature and format of output:

ntxo = 1, ntpr = 500, ntrx = 1, ntwr = 1000

iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 0

ioutfm = 0, 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 = 1000, nscm = 1000, nrespa = 1

t = 0.00000, dt = 0.00200, vlimit = -1.00000

Langevin dynamics temperature regulation:

ig = 71277

temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000

Pressure regulation:

ntp = 1

pres0 = 1.00000, comp = 44.60000, taup = 1.00000

SHAKE:

ntc = 2, jfastw = 0

tol = 0.00001

| 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 = 115.709 Box Y = 115.709 Box Z = 115.709

Alpha = 109.471 Beta = 109.471 Gamma = 109.471

NFFT1 = 120 NFFT2 = 120 NFFT3 = 120

Cutoff= 10.000 Tol =0.100E-04

Ewald Coefficient = 0.27511

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

--------------------------------------------------------------------------------

3. ATOMIC COORDINATES AND VELOCITIES

--------------------------------------------------------------------------------

 begin time read from input coords = 400.000 ps

 Number of triangulated 3-point waters found: 35215

Sum of charges from parm topology file = -0.00000042

Forcing neutrality...



"its hanging at this line"



Thanking you


-- 
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India
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Received on Thu Mar 14 2013 - 08:30:03 PDT
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