AMBER Archive (2004)

Subject: Re: AMBER: simulated annealing..

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Jul 28 2004 - 09:06:01 CDT

1) you might want to use constant volume for 400K simulations
2) maybe try a smaller coupling constant for T (tautp=0.1)
otherwise I don't see any obvious problems

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Abd Ghani Bin Abd Aziz wrote:

>Dear Amber,
>
>sorry..i forgot to type my problem... i already create a new script with
>nmropt=1. i also removed the group definition (as your advice-actually i
>want to restraint but at mean time i just want to see wether the
>temperature can cool down or not). the script that i create, i put it at
>the bottom of the email. as u mention about the output file, it seems that
>everything is fine... but actually the problem still occured..the
>temperature heat up untill 200++K and there at the end of simulation, the
>temperature is still maintain (not recool to 10K)..
>
>i paste also the output file for you to look at it..
>
>thank you.
>
>Abd Ghani
>
># Control section
>&cntrl
>ntwx = 250, ntpr = 50,
>ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,
>scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,
>ntb = 2, ntc = 2, ntf = 2,
>nstlim = 21000, dt = 0.0010,
>ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
>ibelly = 0, ntr = 0,
>imin = 0, irest = 0, ntx = 1, nmropt = 1,
>&end
>
>&ewald
>skinnb = 2.0,
>nbflag = 1,
>&end
>
>&wt
>type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,
>&end
>
>&wt
>type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =
>400.0,
>&end
>
>&wt
>type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =
>10.0,
>&end
>
>&wt
>type='END'
>&end
>&rst
>iat = 0,
>&end
>END
>
>________________________________________________________________________
>
>Here is the input file:
>
>
># Control section
>&cntrl
>ntwx = 250, ntpr = 50,
>ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,
>scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,
>ntb = 2, ntc = 2, ntf = 2,
>nstlim = 21000, dt = 0.0010,
>ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
>ibelly = 0, ntr = 0,
>imin = 0, irest = 0, ntx = 1, nmropt = 1,
>&end
>
>&ewald
>skinnb = 2.0,
>nbflag = 1,
>&end
>
>&wt
>type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,
>&end
>
>&wt
>type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =
>400.0,
>&end
>
>&wt
>type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =
>10.0,
>&end
>
>&wt
>type='END'
>&end
>&rst
>iat = 0,
>&end
>END
>-------------------------------------------------------------------------
>
>
>
>
>
>1. RESOURCE USE:
>
>getting box info from bottom of parm
>getting new box info from bottom of inpcrd
>| peek_ewald_inpcrd: Box info found
>
>EWALD SPECIFIC INPUT:
>
>Largest sphere to fit in unit cell has radius = 32.575
>Calculating ew_coeff from dsum_tol,cutoff
>Box X = 79.791 Box Y = 79.791 Box Z = 79.791
>Alpha = 109.471 Beta = 109.471 Gamma = 109.471
>NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
>Cutoff= 8.000 Tol =0.100E-04
>Ewald Coefficient = 0.34864
>Interpolation order = 4
>
>NATOM = 33896 NTYPES = 17 NBONH = 31021 MBONA = 2952
>NTHETH = 6594 MTHETA = 4023 NPHIH = 11772 MPHIA = 7184
>NHPARM = 0 NPARM = 0 NNB = 69551 NRES = 9744
>NBONA = 2952 NTHETA = 4023 NPHIA = 7184 NUMBND = 44
>NUMANG = 94 NPTRA = 33 NATYP = 30 NPHB = 1
>IFBOX = 2 NMXRS = 24 IFCAP = 0
>
>
>EWALD MEMORY USE:
>
>| Total heap storage needed = 1245
>| Adjacent nonbond minimum mask = 69551
>| Max number of pointers = 25
>| List build maxmask = 139102
>| Maximage = 49591
>
>EWALD LOCMEM POINTER OFFSETS
>| Real memory needed by PME = 1245
>| Size of EEDTABLE = 20918
>| Real memory needed by EEDTABLE = 83672
>| Integer memory needed by ADJ = 139102
>| Integer memory used by local nonb= 1232919
>| Real memory used by local nonb = 555525
>
>| MAX NONBOND PAIRS = 100000000
>
>| Memory Use Allocated Used
>| Real 10000000 1963082
>| Hollerith 10000000 213122
>| Integer 10000000 2119605
>
>| Max Nonbonded Pairs:********
>
>BOX TYPE: TRUNCATED OCTAHEDRON
>
>
>2. CONTROL DATA FOR THE RUN
>
>
>
>TIMLIM= 999999. IREST = 0 IBELLY= 0
>IMIN = 0
>IPOL = 0
>
>NTX = 1 NTXO = 1
>IG = 71277 TEMPI = 10.00 HEAT = 0.000
>
>NTB = 2 BOXX = 79.791
>BOXY = 79.791 BOXZ = 79.791
>
>NTT = 1 TEMP0 = 400.000
>DTEMP = 0.000 TAUTP = 1.000
>VLIMIT= 0.000
>
>NTP = 1 PRES0 = 1.000 COMP = 44.600
>TAUP = 0.100 NPSCAL= 0
>
>NTCM = 0 NSCM = 9999999
>
>NSTLIM=21000 NTU = 1
>T = 0.000 DT = 0.00100
>
>NTC = 2 TOL = 0.00001 JFASTW = 0
>
>NTF = 2 NSNB = 25
>
>CUT = 8.000 SCNB = 2.000
>SCEE = 1.200 DIELC = 1.000
>
>NTPR = 50 NTWR = 50 NTWX = 250
>NTWV = 0 NTWE = 0 IOUTFM= 0
>NTWPRT= 0 NTWPR0= 0 NTAVE= 0
>
>NTR = 0 NTRX = 1
>TAUR = 0.00000 NMROPT= 1 PENCUT= 0.10000
>
>IVCAP = 0 MATCAP= 0 FCAP = 1.500
>
>OTHER DATA:
>
>IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
>XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
>
>VRAND= 0
>
>NATOM = 33896 NRES = 9744
>
>Water definition for fast triangulated model:
>Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
>
>3. ATOMIC COORDINATES AND VELOCITIES
>
>
>begin time read from input coords = 0.000 ps
>
>
>
>Begin reading energy term weight changes/NMR restraints
>WEIGHT CHANGES:
>TEMP0 1 2000 10.000000 400.000000 0 0
>TEMP0 2001 3000 400.000000 400.000000 0 0
>TEMP0 3001 21000 400.000000 10.000000 0 0
>
>RESTRAINTS:
>No valid redirection requests found
>** No restraint defined **
>
>Done reading weight changes/NMR restraints
>
>
>Number of triangulated 3-point waters found: 9377
>
>Sum of charges from parm topology file = -0.00000023
>Forcing neutrality...
>---------------------------------------------------
>APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>using 5000.0 points per unit in tabled values
>TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>| CHECK switch(x): max rel err = 0.3242E-14 at 2.436720
>| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960
>---------------------------------------------------
>Total number of mask terms = 59876
>Total number of mask terms = 119752
> | Total Ewald setup time = 0.09999990
>------------------------------------------------------------------------------
>
>
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