Dear Carlos Simmerling, Adrian Roitberg, or other developer,
I thank you very much for your quick answer. I actually figured out the problem
for simulated annealing and GB implicit solvation with a Berendsen weak coupling
thermostat. I was not checking far enough in time.
SA now works fine, although there is always an initial temperature jump, even if
I start SA with a temperature of 0 K. The temperature jumps up about 35K in the
first 200 steps, decreases to reach 0 again around step 8000 and then rises in
function of the ramp defined in the SA section of the input file. For reminder,
I am simulating a 12bp rna tetraloop (8 bps being involved in watson-crick
h-bonding patterns), without counterions, no cutoff (set to 1000 A) and a
timestep of 1.5 fs).
But SA doesn't work for the same input file, in which I replace the Berendsen
thermostat (NTT=1) by Langevin dynamics (NTT=3) with the collision frequency
(GAMMA_LN) set to 91. The temperature jumps from 0 to 300 K in 50 steps and
doesn't change for the rest of the simulation. At the end, you can find the
input and output of this trial. I just would like a confirmation of the
following message, found in the mailing list. Is SA not possible with Langevin
dynamics?
Thanks in advance!
Pascal
----------------------------------------------------------------
From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 31 2004 - 23:43:01 CDT
* Previous message: David A. Case: "Re: AMBER: Updating Amber 7"
* In reply to: Madalin Giambasu: "AMBER: temperature scaling with
ntt=3(Langevin thermostat)"
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
On Mon, Aug 30, 2004, Madalin Giambasu wrote:
>
> I have a problem with temeperature weighting for Langevin Thermostat: I
> try to heat slowly, but on the output the temperature seems to rise very
> rapidly.
You can't heat "slowly" using a Langevin thermostat (at least as implemented
in Amber). You would need either to change the target temperature very
slowly, or use ntt=1 and the tautp parameter to determine the speed of
heating.
....good luck...dac
------------------------------------------------------
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
-----------------------------------------------------------------------
-------------------------------------------------------
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 19 2005 - 22:53:00 PDT
