no, this is fine. min only writes a restart at the end.
the manual says "every ntwr steps during dynamics" and "written every nstlim
steps for both dynamics and minimization". this could be more clear I guess
that it isn't done each ntwr in minimization.
On Wed, Apr 8, 2009 at 5:45 PM, <taufik.alsarraj.utoronto.ca> wrote:
> 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 - 01:11:15 PDT
