Hi,
I am trying to write a .rst file during a minimization using this *.in file
System minimization -only Si atoms at the surface are fixed
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 1,
ntr = 1,
ntwr = -200,
restraint_wt=10.0,
restraintmask=':1.%Si',
cut = 10
/
this should theoretically write a new rst file every 200 steps. but it
does not. only one rst file is written at the end of the minimization.
Am i missing something?
i use
>
mpirun -np 8 -hostfile ../hostfile_node1 sander.MPI -O -i min2.in -o
\ system5.out -p system3.prmtop -c system4.rst \
-r system5.rst -ref system4.rst
The minimization runs fine, the *.out looks good
File Assignments:
| MDIN: min2.in
| MDOUT: system5.out
|INPCRD: system4.rst
| PARM: system3.prmtop
|RESTRT: system5.rst
| REFC: system4.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
System minimization -only Si atoms at the surface are fixed
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 1,
ntr = 1,
ntwr = -200,
restraint_wt=10.0,
restraintmask=':1.%Si',
cut = 10
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 35.252
| New format PARM file being parsed.
| Version = 1.000 Date = 04/07/09 Time = 10:07:39
NATOM = 68429 NTYPES = 20 NBONH = 65885 MBONA = 2817
NTHETH = 3786 MTHETA = 4633 NPHIH = 5521 MPHIA = 7887
NHPARM = 0 NPARM = 0 NNB = 109031 NRES = 21452
NBONA = 2817 NTHETA = 4633 NPHIA = 7887 NUMBND = 53
NUMANG = 111 NPTRA = 51 NATYP = 37 NPHB = 1
IFBOX = 1 NMXRS = 3520 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 4670468
| Hollerith 432028
| Integer 1789600
| Max Pairs 4926888
| nblistReal 821148
| nblist Int 2361920
| Total 80053 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
MOL
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr
= -200
iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 10000, ncyc = 5000, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 70.504 Box Y = 97.755 Box Z = 119.727
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 72 NFFT2 = 100 NFFT3 = 120
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
MOL
Mask :1.%Si; matches 320 atoms
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Received on Fri Apr 10 2009 - 01:11:14 PDT
