AMBER Archive (2009)

Subject: Re: [AMBER] ntwr

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Apr 08 2009 - 17:45:57 CDT

i was quoting amber10. i think the meaning of the part you quote is that in
md you can save a series of files to minimize later. it doesn't mean that
min will save multiple files. ntwr is only active in md as far as I can
tell.

On Wed, Apr 8, 2009 at 6:35 PM, <taufik.alsarraj_at_utoronto.ca> wrote:

> 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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