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.epfl.ch
Room BCH 4121, Avenue Forel,
http://lcbcpc21.epfl.ch
CH-1015 Lausanne
*******************************************************************************
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Apr 18 2005 - 16:53:00 PDT
