AMBER Archive (2002)

Subject: simulated annealing example

From: Snyder, James (zyu4_at_cdc.gov)
Date: Wed Jul 10 2002 - 15:42:43 CDT

Greetings:

I am attempting to run a simulated annealing calc. using the sample input
file as it EXACTLY appears on page 135 of the AMBER7 manual. I have
prepared prmtop and inpcrd files from leap for a unsolvated ~6000 atom
protein, and did not generate a periodic box since the apparent plan is to
do a non-periodic calculation. I have included the output file, which
displays the error message I receive at the bottom. If I do create a
periodic box (using setbox unit vdw), the calculation proceeds when the
resulting prmtop and inpcrd files are used, but the program ignores most of
the settings in the control list, eg. ntb becomes 1 even though I set it to
0 etc. and is obviously not a solution.

???????

Thank You,
Jim Snyder
zyu4_at_cdc.gov

          -------------------------------------------------------
          Amber 7 SANDER Scripps/UCSF 2002
          -------------------------------------------------------

| Wed Jul 10 16:17:53 2002

  [-O]verwriting output

File Assignments:
| MDIN: 1fv1_sa.in

| MDOUT: 1fv1_sa.out

|INPCRD: 1fv1_sa.crd

| PARM: 1fv1_sa.top

|RESTRT: 1fv1_sa.rst

| REFC: 1fv1_sa.crd

| MDVEL: mdvel

| MDEN: mden

| MDCRD: 1fv1_sa.traj

|MDINFO: mdinfo

|INPDIP: inpdip

|RSTDIP: rstdip

 
 Here is the input file:
 
15ps simulated annealing protocol

  &cntrl

    nstlim=15000, ntt=1, (time limit, temp. control)

    scee=1.2, (scee holds the 1-4 scale factor)

    ntpr=500, pencut=0.1, (control of printout)

    ipnlty=1, nmropt=1, (NMR penalty function options)

    vlimit=10, (prevent bad temp. jumps)

    ntb=0, (non-periodic simulation)

  &end

#

# Simple simulated annealing algorithm:

#

# from steps 0 to 1000: raise target temperature 10->1200K

# from steps 1000 to 3000: leave at 1200K

# from steps 3000 to 15000: re-cool to low temperatures

#

 &wt type='TEMP0', istep1=0,istep2=1000,value1=10.,

             value2=1200., &end

 &wt type='TEMP0', istep1=1001, istep2=3000, value1=1200.,

             value2=1200.0, &end

 &wt type='TEMP0', istep1=3001, istep2=15000, value1=0.,

             value2=0.0, &end

#

# Strength of temperature coupling:

#

# steps 0 to 3000: tight coupling for heating and equilibration

# steps 3000 to 11000: slow cooling phase

# steps 11000 to 13000: somewhat faster cooling

# steps 13000 to 15000: fast cooling, like a minimization

#

 &wt type='TAUTP', istep1=0,istep2=3000,value1=0.2,

             value2=0.2, &end

 &wt type='TAUTP', istep1=3001,istep2=11000,value1=4.0,

             value2=2.0, &end

 &wt type='TAUTP', istep1=11001,istep2=13000,value1=1.0,

             value2=1.0, &end

 &wt type='TAUTP', istep1=13001,istep2=14000,value1=0.5,

             value2=0.5, &end

 &wt type='TAUTP', istep1=14001,istep2=15000,value1=0.05,

             value2=0.05, &end

        

#

# "Ramp up" the restraints over the first 3000 steps:

#

 &wt type='REST', istep1=0,istep2=3000,value1=0.1,

             value2=1.0, &end

 &wt type='REST', istep1=3001,istep2=15000,value1=1.0,

             value2=1.0, &end

        

 &wt type='END' &end

LISTOUT=POUT

DISANG=RST.f

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

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

| Flags: SGIFFT MEM_ALLOC MPI RLE ROWAT HAS_FTN_ERFC

 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info not found in inpcrd
 compute_nfft: failed to get good fft array size
 x =  4.93287768640256299E+24