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 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu