Dear Prof. Case,
I thank you very much for your answer.
I actually use Langevin dynamics on my rna system because the sampling stays
pretty much closer to the nmr structure as compared to Berendsen dynamics,
result that by the way matches to simulations reported in the litterature. But
the SA simply does not work, it jumps very quickly from 0 to 300 degrees K. It
works fine for the Berendsen dynamics, though. I would like to know whether I
forgot anything in the input file (end of the email), or whether SA simply is
not made to work with langevin dynamics in amber8 (as suggested by one of your
messages concerning this issue, in the mailing list archives:
http://amber.ch.ic.ac.uk/archive/200409/0011.html ).
I would guess the thermostat temperature control for langevin dynamics is done
via the random collision force, that is taken from a temperature dependant
gaussian distribution, as suggested in van Gunstern et al., 1981. If that is the
implementation in amber8, I suppose simulated annealing could be performed by
slowly varying the temperature of the gaussian distribution yielding the random
collision force? But that might not be implemented..
One last question, if you will: Supposing there's no SA for langevin dynamics, I
should apply the trick you suggested me in your last email, that I recopy here
below:
To use Langevin dynamics, you could set a series of target temperatures,
(say 600, 500, 400, 300, 200, 100, 10, etc.) to take effect at different times
during the simulation. This could have the effect of fairly slow cooling.
But the Berendsen approach seems to me to be a more natural way of carrying
out simulated annealing.
Practically speaking, you mean there would be one simulation for each of these
temperatures, so that in the end I would have to paste the trajectory and energy
files? Or are there any tools to do that in one single simulation in amber?
Thank you very much!
Pascal
------------------------------------------------------
equilibr
&cntrl
IMIN = 0,
NMROPT = 1,
NTX = 1,
IREST = 0,
NTPR = 10,
NTWR = 10000,
NTWX = 500,
NTF = 1,
NTB = 0,
DIELC = 1.0,
CUT = 1000.0,
SCNB = 2.0,
SCEE = 1.2,
NSTLIM = 32000000,
NSCM = 1000,
DT = 0.0015,
NTT = 3,
GAMMA_LN = 91,
TEMPI=0.0
NTC = 2,
TOL = 0.00001,
NTR = 0,
IBELLY = 0,
IVCAP = 0,
IGB = 1,
&end
&wt
TYPE='TEMP0', istep1=0, istep2=400000, value1=0.0, value2=300.0,
&end
&wt
TYPE='TEMP0', istep1=400001, istep2=32000000, value1=300.0, value2=300.0,
&end
&wt
TYPE='END',
&end
-----------------------------------------------------------------------
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 04/19/2005 at 22:25:28
File Assignments:
| MDIN: saLang.in
| MDOUT: mdout
|INPCRD: ../../min/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,
NMROPT = 1,
NTX = 1,
IREST = 0,
NTPR = 10,
NTWR = 10000,
NTWX = 500,
NTF = 1,
NTB = 0,
DIELC = 1.0,
CUT = 1000.0,
SCNB = 2.0,
SCEE = 1.2,
NSTLIM = 32000000,
NSCM = 1000,
DT = 0.0015,
NTT = 3,
GAMMA_LN = 91,
TEMPI=0.0
NTC = 2,
TOL = 0.00001,
NTR = 0,
IBELLY = 0,
IVCAP = 0,
IGB = 1,
&end
&wt
TYPE='TEMP0', istep1=0, istep2=400000, value1=0.0, value2=300.0,
&end
&wt
TYPE='TEMP0', istep1=400001, istep2=1000000, value1=300.0, value2=300.0,
&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 = 1, irest = 0, 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 =32000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00150, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 91.00000
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 = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 0 400000 0.000000 300.000000 0 0
TEMP0 4000011000000 300.000000 300.000000 0 0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 196 389
| Running AMBER/MPI version on 2 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -2779.4852 EKtot = 0.0000 EPtot = -2779.4852
BOND = 19.1296 ANGLE = 82.2276 DIHED = 272.9131
1-4 NB = 95.4341 1-4 EEL = -1594.9962 VDWAALS = -231.1730
EELEC = 982.8168 EGB = -2405.8371 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 10 TIME(PS) = 0.015 TEMP(K) = 229.60 PRESS = 0.0
Etot = -2390.9966 EKtot = 234.5205 EPtot = -2625.5170
BOND = 84.5193 ANGLE = 153.2205 DIHED = 292.3035
1-4 NB = 93.9796 1-4 EEL = -1596.0479 VDWAALS = -230.5382
EELEC = 991.2556 EGB = -2414.2094 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 20 TIME(PS) = 0.030 TEMP(K) = 281.06 PRESS = 0.0
Etot = -2253.7608 EKtot = 287.0774 EPtot = -2540.8382
BOND = 98.7574 ANGLE = 203.1569 DIHED = 297.2468
1-4 NB = 100.5581 1-4 EEL = -1599.6456 VDWAALS = -229.6152
EELEC = 998.2835 EGB = -2409.5801 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 30 TIME(PS) = 0.045 TEMP(K) = 296.69 PRESS = 0.0
Etot = -2230.7932 EKtot = 303.0465 EPtot = -2533.8397
BOND = 106.8442 ANGLE = 196.3865 DIHED = 302.9300
1-4 NB = 102.3982 1-4 EEL = -1602.0131 VDWAALS = -225.7046
EELEC = 986.5798 EGB = -2401.2606 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 40 TIME(PS) = 0.060 TEMP(K) = 285.59 PRESS = 0.0
Etot = -2223.0507 EKtot = 291.7026 EPtot = -2514.7533
BOND = 107.3846 ANGLE = 206.2646 DIHED = 306.5084
1-4 NB = 94.2960 1-4 EEL = -1588.1377 VDWAALS = -217.1324
EELEC = 980.1088 EGB = -2404.0455 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 50 TIME(PS) = 0.075 TEMP(K) = 304.90 PRESS = 0.0
Etot = -2214.6613 EKtot = 311.4273 EPtot = -2526.0886
BOND = 117.4039 ANGLE = 194.1453 DIHED = 305.2657
1-4 NB = 101.3505 1-4 EEL = -1610.1342 VDWAALS = -227.5490
EELEC = 1006.3729 EGB = -2412.9437 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 60 TIME(PS) = 0.090 TEMP(K) = 278.82 PRESS = 0.0
Etot = -2233.4890 EKtot = 284.7920 EPtot = -2518.2811
BOND = 97.3556 ANGLE = 212.4408 DIHED = 312.5412
1-4 NB = 101.2733 1-4 EEL = -1597.0333 VDWAALS = -228.1140
EELEC = 993.9940 EGB = -2410.7387 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 70 TIME(PS) = 0.105 TEMP(K) = 298.24 PRESS = 0.0
Etot = -2219.1645 EKtot = 304.6290 EPtot = -2523.7935
BOND = 98.8641 ANGLE = 207.2412 DIHED = 310.1483
1-4 NB = 99.9853 1-4 EEL = -1591.3145 VDWAALS = -231.2306
EELEC = 989.3254 EGB = -2406.8127 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 80 TIME(PS) = 0.120 TEMP(K) = 302.74 PRESS = 0.0
Etot = -2219.9418 EKtot = 309.2247 EPtot = -2529.1664
BOND = 114.6213 ANGLE = 191.7638 DIHED = 311.9104
1-4 NB = 93.1754 1-4 EEL = -1595.5519 VDWAALS = -226.1664
EELEC = 988.4763 EGB = -2407.3953 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 90 TIME(PS) = 0.135 TEMP(K) = 301.51 PRESS = 0.0
Etot = -2196.3292 EKtot = 307.9681 EPtot = -2504.2973
BOND = 108.0526 ANGLE = 211.8796 DIHED = 325.4895
1-4 NB = 102.1647 1-4 EEL = -1600.5646 VDWAALS = -228.9878
EELEC = 974.0873 EGB = -2396.4186 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 100 TIME(PS) = 0.150 TEMP(K) = 285.78 PRESS = 0.0
Etot = -2209.3252 EKtot = 291.8961 EPtot = -2501.2213
BOND = 114.9016 ANGLE = 210.9523 DIHED = 320.3746
1-4 NB = 96.5399 1-4 EEL = -1598.1488 VDWAALS = -223.0011
EELEC = 981.2488 EGB = -2404.0886 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 110 TIME(PS) = 0.165 TEMP(K) = 303.40 PRESS = 0.0
Etot = -2220.6197 EKtot = 309.8963 EPtot = -2530.5160
BOND = 106.4613 ANGLE = 200.1546 DIHED = 302.1341
1-4 NB = 103.5301 1-4 EEL = -1588.6475 VDWAALS = -228.9083
EELEC = 975.1808 EGB = -2400.4211 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 120 TIME(PS) = 0.180 TEMP(K) = 305.10 PRESS = 0.0
Etot = -2201.7270 EKtot = 311.6302 EPtot = -2513.3572
BOND = 104.4586 ANGLE = 210.9078 DIHED = 307.6163
1-4 NB = 103.1315 1-4 EEL = -1567.2926 VDWAALS = -224.8680
EELEC = 935.0566 EGB = -2382.3675 RESTRAINT = 0.0000
------------------------------------------------------------------------------
*******************************************************************************
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
*******************************************************************************
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Received on Tue Apr 26 2005 - 11:53:00 PDT
