AMBER Archive (2009)

Subject: RE: [AMBER] please help me out

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Mar 14 2009 - 11:54:22 CDT

Hi Bharat,

Chances are that your initial structure is bad and this is causing some
division by zero somewhere that is giving an infinite energy and causing the
code to crash. Unfortunately when running in parallel such problems can be
hard to detect and error messages can get lost in places and output not
generated. This occurs because only one of the threads likely crashed and
the others are waiting at a barrier somewhere and so the code appears to
hang. In such cases it is advisable to try things out in serial and see what
happens. At least here you will be able to see any error messages etc.

I would also just try running the first 100 steps or so of minimization and
set ntpr=1. In that way you will be able to see if any problems exist with
the initial structure and possibly track them down.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of bharat lakhani
> Sent: Saturday, March 14, 2009 4:05 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] please help me out
>
> Respected sir,
> When i am running sander for my complex
> minimization.It is generating following output.
>
>
> -------------------------------------------------------
> Amber 9 SANDER 2006
> -------------------------------------------------------
>
> | Run on 03/07/2009 at 06:02:48
> [-O]verwriting output
>
> File Assignments:
> | MDIN: minvac.in
>
> | MDOUT:
> DRUG0minvac.out
> |INPCRD:
> DRUG0.crd
> | PARM:
> DRUG0.top
> |RESTRT:
> DRUG0minvac.crd
> | REFC:
> refc
> | MDVEL:
> mdvel
> | MDEN:
> mden
> | MDCRD:
> mdcrd
> |MDINFO:
> mdinfo
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
>
> Here is the input file:
>
> in vacuo
> minimization
> &cntrl
>
> imin =
> 1,
> maxcyc =
> 1000,
> ncyc =
> 200,
> ntb =
> 0,
> igb =
> 0,
> cut =
> 12
> /
>
>
> --------------------------------------------------------------------------
> ------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------
> ------
>
> | Flags:
> MPI
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> |Largest sphere to fit in unit cell has radius = 49.070
> | New format PARM file being parsed.
> | Version = 1.000 Date = 03/07/09 Time = 06:02:30
> NATOM = 2506 NTYPES = 15 NBONH = 1241 MBONA = 1297
> NTHETH = 2798 MTHETA = 1764 NPHIH = 5299 MPHIA = 3375
> NHPARM = 0 NPARM = 0 NNB = 13749 NRES = 160
> NBONA = 1297 NTHETA = 1764 NPHIA = 3375 NUMBND = 52
> NUMANG = 108 NPTRA = 43 NATYP = 38 NPHB = 0
> IFBOX = 0 NMXRS = 39 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 160042
> | Hollerith 15198
> | Integer 249443
> | Max Pairs 1443456
> | nblistReal 30072
> | nblist Int 1046806
> | Total 12246 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> --------------------------------------------------------------------------
> ------
> 2. CONTROL DATA FOR THE RUN
> --------------------------------------------------------------------------
> ------
>
>
>
>
> 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 =
> 500
> iwrap = 0, ntwx = 0, ntwv = 0, ntwe
> = 0
> ioutfm = 0, ntwprt = 0, idecomp = 0,
> rbornstat= 0
>
> Potential function:
> ntf = 1, ntb = 0, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 1000, ncyc = 200, ntmin = 1
> dx0 = 0.01000, drms = 0.00010
> | INFO: Old style inpcrd file read
>
>
> --------------------------------------------------------------------------
> ------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------
> ------
>
>
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 0
> | Atom division among processors:
> | 0 322 632 948 1270 1570 1879 2201
> | 2506
>
> Sum of charges from parm topology file = -1.00003006
> | Running AMBER/MPI version on 8 nodes
>
>
> --------------------------------------------------------------------------
> ------
> 4. RESULTS
> --------------------------------------------------------------------------
> ------
>
> ---------------------------------------------------
>
> eedmeth=4: Setting switch to one everywhere
>
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 66786
> | TOTAL SIZE OF NONBOND LIST = 524450
>
> Why it is not minimizing my complex.i do not know.my be the cavity size of
> my complex is not as much as it has to be.please help me out

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