AMBER Archive (2009)

Subject: Re: [AMBER] ntwr

From: taufik.alsarraj_at_utoronto.ca
Date: Wed Apr 08 2009 - 17:35:57 CDT

Hi Carlos,
but in the manual it says if NTWR<0, a unique copy of the file .... is
written every abs(NTWR) steps. this option... or save a series of
restrt files for minimization.
i would like to save a series of rst files for minimization. i did not
use this option in AMBER 9 so i don't know if it has changed.

Quoting Carlos Simmerling <carlos.simmerling_at_gmail.com>:

> 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_at_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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