AMBER Archive (2005)

Subject: Re: AMBER: langevin, GB and simulated annealing?

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Apr 18 2005 - 10:36:19 CDT

first try a smaller temperature coupling constant for the
normal GB and see if that helps- 1.0 is quite
weak for doing annealing. Try 0.1 or even 0.01
to test to make sure it is working.

one problem with the input you sent is that you have not defined
temp0 beyond step 1000.

I'm not sure why you included the output from step 10- is
there something we should see there?

pascal.baillod_at_epfl.ch wrote:

>Dear Amber developers,
>
>I am trying to use Amber8 for a GB implicit solvent simulation with langevin
>dynamics (ntt=3) of a 12 bp rna tetraloop. I would like to use simulated
>annealing (SA), but whatever I do the temperature stays at 300.0. I read a
>message on the mailing list that says that SA is not possible with langevin
>dynamics. So I tried the same with the berendsen thermostat (ntt=1), but again,
>no change in temperature. With explicit solvent, however, it works. Dose that
>mean SA is not implemented for GB and/or langevin? You can find my input and
>ouput here below. The latter seems to confirm that the SA weight change input
>was read in..
>
>Thank you very much for your help!
>
>Pascal
>
>
>equilibr
> &cntrl
> IMIN = 0,
> NTX = 5,
> IREST = 1,
> NTPR = 10,
> NMROPT = 1,
> NTWR = 10000,
> NTWX = 500,
> NTF = 1,
> NTB = 0,
> DIELC = 1.0,
> CUT = 1000.0,
> SCNB = 2.0,
> SCEE = 1.2,
> NSTLIM = 2000000,
> NSCM = 1000,
> DT = 0.0015,
> NTT = 1,
> NTC = 2,
> TOL = 0.00001,
> NTR = 0,
> IBELLY = 0,
> IVCAP = 0,
> IGB = 1,
> VLIMIT=10,
> &end
> &ewald
> eedmeth=4,
> &end
> &wt
> TYPE='TEMP0', istep1=0, istep2=200, value1=300.0, value2=400.0,
> &end
> &wt
> TYPE='TEMP0', istep1=201, istep2=1000, value1=400.0, value2=400.0,
> &end
> &wt
> TYPE='END'
> &end
>
>
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
>| Run on 04/17/2005 at 22:34:18
>
>File Assignments:
>| MDIN: 2test.in
>| MDOUT: mdout
>|INPCRD: ../ERR-SA/2langev/mdres.crd
>| PARM: ../../ff99.top
>|RESTRT: mdres.crd
>| REFC: refc
>| MDVEL: mdvel
>| MDEN: mden
>| MDCRD: traj.crd
>|MDINFO: mdinfo
>|INPDIP: inpdip
>|RSTDIP: rstdip
>
>
> Here is the input file:
>
>equilibr
> &cntrl
> IMIN = 0,
> NTX = 5,
> IREST = 1,
> NTPR = 10,
> NMROPT = 1,
> NTWR = 10000,
> NTWX = 500,
> NTF = 1,
> NTB = 0,
> DIELC = 1.0,
> CUT = 1000.0,
> SCNB = 2.0,
> SCEE = 1.2,
> NSTLIM = 2000000,
> NSCM = 1000,
> DT = 0.0015,
> NTT = 1,
> NTC = 2,
> TOL = 0.00001,
> NTR = 0,
> IBELLY = 0,
> IVCAP = 0,
> IGB = 1,
> VLIMIT=10,
> &end
> &ewald
> eedmeth=4,
> &end
> &wt
> TYPE='TEMP0', istep1=0, istep2=200, value1=300.0, value2=400.0,
> &end
> &wt
> TYPE='TEMP0', istep1=201, istep2=1000, value1=400.0, value2=400.0,
> &end
> &wt
> TYPE='END'
> &end
>
>--------------------------------------------------------------------------------
> 1. RESOURCE USE:
>--------------------------------------------------------------------------------
>
>| Flags: MPI
>| New format PARM file being parsed.
>| Version = 1.000 Date = 03/18/05 Time = 18:11:40
> NATOM = 389 NTYPES = 14 NBONH = 133 MBONA = 286
> NTHETH = 301 MTHETA = 445 NPHIH = 658 MPHIA = 812
> NHPARM = 0 NPARM = 0 NNB = 2166 NRES = 12
> NBONA = 286 NTHETA = 445 NPHIA = 812 NUMBND = 35
> NUMANG = 72 NPTRA = 39 NATYP = 24 NPHB = 0
> IFBOX = 0 NMXRS = 34 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
>| Memory Use Allocated
>| Real 11134
>| Hollerith 2348
>| Integer 40875
>| Max Pairs 1
>| Max Rstack 1
>| Max Istack 1
>| Total 255 kbytes
>| Duplicated 0 dihedrals
>| Duplicated 0 dihedrals
>
>--------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>--------------------------------------------------------------------------------
>
>
>
>General flags:
> imin = 0, nmropt = 1
>
>Nature and format of input:
> ntx = 5, irest = 1, ntrx = 1
>
>Nature and format of output:
> ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 10000
> iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 0
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
>
>Potential function:
> ntf = 1, ntb = 0, igb = 1, nsnb = 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut =1000.00000, intdiel = 1.00000
> saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
> gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
> rdt = 0.00000, rgbmax = 25.00000
> scnb = 2.00000, scee = 1.20000
>
>Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
>Molecular dynamics:
> nstlim = 2000000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00150, vlimit = 10.00000
>
>Berendsen (weak-coupling) temperature regulation:
> temp0 = 300.00000, tempi = 0.00000, tautp = 1.00000
>
>SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
>
>NMR refinement options:
> iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1
> scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
>
>--------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>--------------------------------------------------------------------------------
>
>
> begin time read from input coords = 3000.000 ps
>
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> TEMP0 0 200 300.000000 400.000000 0 0
> TEMP0 201 1000 400.000000 400.000000 0 0
>
> RESTRAINTS:
> ** No restraint defined **
>
> Done reading weight changes/NMR restraints
>
>
> Number of triangulated 3-point waters found: 0
>| Atom division among processors:
>| 0 389
>| Running AMBER/MPI version on 1 nodes
>
>
>--------------------------------------------------------------------------------
> 4. RESULTS
>--------------------------------------------------------------------------------
>
>
> NSTEP = 10 TIME(PS) = 3000.015 TEMP(K) = 313.74 PRESS = 0.0
> Etot = -2193.2307 EKtot = 320.4587 EPtot = -2513.6894
> BOND = 109.3584 ANGLE = 235.9093 DIHED =
>
>
>*******************************************************************************
>Pascal Baillod (PhD student)
>*******************************************************************************
>Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
>Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
>Laboratory of Computational Chemistry and Biochemistry pascal.baillod_at_epfl.ch
>Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
>CH-1015 Lausanne
>*******************************************************************************
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

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