Dear Daniel Roe and David A Case
Thanks for your useful reply. I used the parmed.py (I do minimization
again with new files ionicbox2.* successfully), but the output file maybe
has some defect, for example the .incprd file does not include the box
information, or when the box information was add to end of the file an
error that is related to periodicity was appeared. Also I change the ifbox
to one (the 28th number in %FLAG POINTERS %FORMAT(10I8) in prmtop file ),
but again the fallowing error was appeared?
Is it possible to fix the file completely?
Your Sincerely
S. Nasiri
======================parmed.py============================
parmed.py -p ionicbox.prmtop
./ | | \.
.:( |i __ j| ):`.
.' `._ |`::::'| _.' `.
.' "---.j `::' f.---" `.
_____/ ___ ____ __ __ ____ ___
| \ | | | `__'| \ / || | | \
| .-. | .' `| | .-. |-/| \/ || ___| | . \
| |_| | | i | | |_| /"":| || | | | \ \
| / | .^. | | /::::| || |__. | | \ \
| ----' | | | | | \ :: | || __| | | | )
| | .' ''' `.| |\ \ | i i j| | . | / /
| | | _ || | \ \ | |\/| || |__. | |. / .
[| | | | | || | \ \ | | | || | | / ].
] `--' :--' `--::--' \_|`--' ::--"|____|-"-- / :[
| __ ::-'''`.:' "--. .----::.----:: ,.---._ :|
[ .-"" "`' \ / " `' `-. :].
]:.' \/ `.:[
|/ \|
ParmEd: a Parameter file Editor
Loaded Amber topology file ionicbox.prmtop
Reading input from STDIN...
> loadRestrt ionicbox.inpcrd
Loading restart file ionicbox.inpcrd
> checkValidity
Determining validity of prmtop
1 total warnings
FixableParmWarning: sum(ATOMS_PER_MOLECULE) != NATOM. Use "setMolecules" to
fix
this
> setMolecules ATOMS_PER_MOLECULE=true
/home/nasiri/amber12/bin/ParmedTools/ParmedActions.py:879: UserWarning:
Value of solute_ions is unrecognized [ATOMS_PER_MOLECULE=true]! Assuming
True
solute_ions + "Assuming True")
Setting MOLECULE properties of the prmtop (SOLVENT_POINTERS and
ATOMS_PER_MOLECULE)
> outparm ionicbox2.prmtop ionicbox2.inpcrd
Outputting Amber topology file ionicbox2.prmtop and restart ionicbox2.inpcrd
> quit
Done!
=====================pmemd.MPI============================
mpirun -np 4 pmemd.MPI -O -i mdin.in -o md1.out -p ionicbox2.prmtop -c
min.x -r md1.x -x md1.nc -e md1.dat
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
libmpi.so.1 00007F7B5530BDB2 Unknown Unknown Unknown
libmpi.so.1 00007F7B5523E9A2 Unknown Unknown Unknown
mca_coll_tuned.so 00007F7B4DF670B0 Unknown Unknown Unknown
mca_coll_tuned.so 00007F7B4DF66CCD Unknown Unknown Unknown
mca_coll_tuned.so 00007F7B4DF5DD9D Unknown Unknown Unknown
mca_coll_sync.so 00007F7B4E17C64D Unknown Unknown Unknown
libmpi.so.1 00007F7B5524D14D Unknown Unknown Unknown
libmpi_f77.so.1 00007F7B555FC106 Unknown Unknown Unknown
pmemd.MPI 0000000000526634 Unknown Unknown Unknown
pmemd.MPI 000000000041E48C Unknown Unknown Unknown
libc.so.6 00007F7B52AC276D Unknown Unknown Unknown
pmemd.MPI 000000000041E389 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
mca_btl_sm.so 00007F189A6D53C9 Unknown Unknown Unknown
libmpi.so.1 00007F18A0BB5E39 Unknown Unknown Unknown
libmpi.so.1 00007F18A0AE89A2 Unknown Unknown Unknown
mca_coll_tuned.so 00007F18998112A4 Unknown Unknown Unknown
mca_coll_tuned.so 00007F1899810CCD Unknown Unknown Unknown
mca_coll_tuned.so 00007F1899807D9D Unknown Unknown Unknown
mca_coll_sync.so 00007F1899A2664D Unknown Unknown Unknown
libmpi.so.1 00007F18A0AF714D Unknown Unknown Unknown
libmpi_f77.so.1 00007F18A0EA6106 Unknown Unknown Unknown
pmemd.MPI 0000000000526634 Unknown Unknown Unknown
pmemd.MPI 000000000041E48C Unknown Unknown Unknown
libc.so.6 00007F189E36C76D Unknown Unknown Unknown
pmemd.MPI 000000000041E389 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
libmpi.so.1 00007FBFEA69DDAB Unknown Unknown Unknown
libmpi.so.1 00007FBFEA5D09A2 Unknown Unknown Unknown
mca_coll_tuned.so 00007FBFE32F92A4 Unknown Unknown Unknown
mca_coll_tuned.so 00007FBFE32F8CCD Unknown Unknown Unknown
mca_coll_tuned.so 00007FBFE32EFD9D Unknown Unknown Unknown
mca_coll_sync.so 00007FBFE350E64D Unknown Unknown Unknown
libmpi.so.1 00007FBFEA5DF14D Unknown Unknown Unknown
libmpi_f77.so.1 00007FBFEA98E106 Unknown Unknown Unknown
pmemd.MPI 0000000000526634 Unknown Unknown Unknown
pmemd.MPI 000000000041E48C Unknown Unknown Unknown
libc.so.6 00007FBFE7E5476D Unknown Unknown Unknown
pmemd.MPI 000000000041E389 Unknown Unknown Unknown
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 4075 on
node nasiri-desktop exiting improperly. There are two reasons this could
occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
=====================md1.out===========================
ionicbox2.inpcrd
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 12
| Run on 02/21/2014 at 12:16:22
[-O]verwriting output
File Assignments:
| MDIN: mdin.in
| MDOUT:
md1.out
| INPCRD:
min.x
| PARM:
ionicbox2.prmtop
| RESTRT:
md1.x
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
md1.dat
| MDCRD: md1.nc
| MDINFO:
mdinfo
|LOGFILE:
logfile
Here is the input file:
&cntrl
imin=0, ntpr=10000,
ntwx=10000,
ntx=1,
irest=0,
tempi=298., temp0=298.,
ntt=3,
gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1,
nstlim=2000000,
ntwr=1000, dt=.001, ig=-1,
cut=12,
&end
Note: ig = -1. Setting random seed based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| Largest sphere to fit in unit cell has radius = 14.992
| New format PARM file being parsed.
| Version = 1.000 Date = 02/21/14 Time = 12:14:56
| 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 = 1744 NTYPES = 10 NBONH = 1144 MBONA = 336
NTHETH = 2056 MTHETA = 96 NPHIH = 1160 MPHIA = 136
NHPARM = 0 NPARM = 0 NNB = 5136 NRES = 264
NBONA = 336 NTHETA = 96 NPHIA = 136 NUMBND = 12
NUMANG = 21 NPTRA = 11 NATYP = 11 NPHB = 0
IFBOX = 0 NMXRS = 26 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 4 4 4
| Direct force subcell size = 7.4997 7.5000 7.4958
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 10000, ntrx = 1, ntwr =
1000
iwrap = 0, ntwx = 10000, ntwv = 0, ntwe
= 0
ioutfm = 1, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 2, igb = 0, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 2000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 861614
temp0 = 298.00000, tempi = 298.00000, gamma_ln= 5.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 10000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 29.999 Box Y = 30.000 Box Z = 29.983
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 30 NFFT2 = 30 NFFT3 = 30
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
| ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
Input errors occurred. Terminating execution.
=====================change IFBOX==========================
ionicbox2.prmtop
********************initial ******************************
%VERSION VERSION_STAMP = V0001.000 DATE = 02/21/14 12:14:56
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
1744 10 1144 336 2056 96 1160 136
0 0
5136 264 336 96 136 12 21 11
11 0
0 0 0 0 0 0 0 0
26 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
*************************next*************************
%VERSION VERSION_STAMP = V0001.000 DATE = 02/21/14 12:14:56
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
1744 10 1144 336 2056 96 1160 136
0 0
5136 264 336 96 136 12 21 11
11 0
0 0 0 0 0 0 0 1
26 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
==================simulation===================================
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 12
| Run on 02/21/2014 at 13:11:34
[-O]verwriting output
File Assignments:
| MDIN: mdin.in
| MDOUT:
md1.out
| INPCRD:
min.x
| PARM:
ionicbox2.prmtop
| RESTRT:
md1.x
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
md1.dat
| MDCRD: md1.nc
| MDINFO:
mdinfo
|LOGFILE:
logfile
Here is the input file:
&cntrl
imin=0, ntpr=10000,
ntwx=10000,
ntx=1,
irest=0,
tempi=298., temp0=298.,
ntt=3,
gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1,
nstlim=2000000,
ntwr=1000, dt=.001, ig=-1,
cut=12,
&end
Note: ig = -1. Setting random seed based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| Largest sphere to fit in unit cell has radius = 14.992
| New format PARM file being parsed.
| Version = 1.000 Date = 02/21/14 Time = 12:14:56
| 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.
ERROR: Flag "SOLVENT_POINTERS" not found in PARM file
================================================================
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Received on Fri Feb 21 2014 - 02:00:02 PST
