AMBER Archive (2005)

Subject: Re: AMBER: lastrst

From: Stern, Julie (jvstern_at_bnl.gov)
Date: Wed Feb 23 2005 - 15:03:57 CST

Thanks for all the help.

I tried it with ibelly = 0 and no ibelly or bellymask altogether and
still the same result.

Thanks, Ilyas for trying out the input file. I don't have a big
structure. It is only 11 atoms, a reduced model in order to understand why
vlimits
were being exceeded and temperature was blowing up. When I tried the
restraining
option as opposed to the belly option, the atoms that I wanted pinned moved
even with higher harmonic force constants, so I went back to belly.

My simulation is also running in vacuo. Maybe that is causing a
problem.

Here is the whole output file as Carlos requested:

localhost 128% more min.out

          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 02/23/2005 at 11:28:13
  [-O]verwriting output

File Assignments:
| MDIN: min.in
| MDOUT: min.out
|INPCRD: ssh1shortchain2.inpcrd
| PARM: ssh1shortchain2.prmtop
|RESTRT: ssh1shortchain2_min.rst
| REFC: ssh1shortchain2.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

minimization
&cntrl
   imin=1,
   ncyc=250,
   maxcyc=1000,
   lastrst=60000000000,
   ntf=1,
   ntc=1,
   ntpr=10,
   igb=0,
   ntb=1,
   cut=3.0,
   ibelly=1,
   bellymask='!@SA',
&end

------------------------------------------------------------------------ 

----
----
   1.  RESOURCE   USE:
------------------------------------------------------------------------
----
----

| Flags:
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius =     5.010
| New format PARM file being parsed.
| Version =    1.000 Date = 02/22/05 Time = 16:40:53
 NATOM  =      11 NTYPES =       4 NBONH =       7 MBONA  =       3
 NTHETH =      16 MTHETA =       2 NPHIH =      17 MPHIA  =       1
 NHPARM =       0 NPARM  =       0 NNB   =      47 NRES   =       1
 NBONA  =       3 NTHETA =       2 NPHIA =       1 NUMBND =       4
 NUMANG =       7 NPTRA  =       5 NATYP =       4 NPHB   =       0
 IFBOX  =       1 NMXRS  =      11 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

|     Memory Use     Allocated
|     Real               89727
|     Hollerith             69
|     Integer            42095
|     Max Pairs             55
|     Max Rstack          3564
|     Max Istack            55
|       Total              893 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

     BOX TYPE: RECTILINEAR

------------------------------------------------------------------------
----
----
   2.  CONTROL  DATA  FOR  THE  RUN
------------------------------------------------------------------------
----
----

SSH

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    =      10, 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     =       1, igb     =       0, nsnb    =
25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     =   3.00000, intdiel =   1.00000
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       1, ntr     =       0

Energy minimization:
     maxcyc  =    1000, ncyc    =     250, 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  =       1
     Box X =   10.020   Box Y =   10.020   Box Z =   10.779
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =   10       NFFT2 =   10       NFFT3 =   10
     Cutoff=    3.000   Tol   =0.100E-04
     Ewald Coefficient =  0.98370
     Interpolation order =    4

Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!

    LOADING THE BELLY ATOMS AS GROUPS

     Mask !@SA; matches    10 atoms

------------------------------------------------------------------------
----
----
   3.  ATOMIC COORDINATES AND VELOCITIES
------------------------------------------------------------------------
----
----

SSH
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0

     Sum of charges from parm topology file =   0.00000100
     Forcing neutrality...

------------------------------------------------------------------------
----
----
   4.  RESULTS
------------------------------------------------------------------------
----
----

 Exceeding lastrst in get_stack
   lastrst =         3564
   top_stk=            0
   isize  =        22133
   request=        22133
  Increase lastrst in the &cntrl namelist
localhost 129%

-----Original Message-----
From: owner-amber_at_scripps.edu
To: amber_at_scripps.edu
Sent: 2/23/2005 12:53 AM
Subject: Re: AMBER: lastrst

On Tue, Feb 22, 2005, Stern, Julie wrote:
>
> Exceeding lastrst in get_stack
>    lastrst =         3564
>    top_stk=            0
>    isize  =        22133
>    request=        22133
>   Increase lastrst in the &cntrl namelist

If this is amber8, it looks like a bug in the code: you are not supposed
to get "lastrst" errors, and there is no simple way to get around it.
It
presumably is arising from some combination of input parameters that is
causing the program to use more memory than it is expecting to.

Does it run if you set ibelly=0?  If you can figure out what triggers
the error, that will help us; otherwise you will probably have to post
the
inputs that you are using.

...good luck...dac 
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