AMBER Archive (2004)

Subject: AMBER: temperature scaling with ntt=3(Langevin thermostat)

From: Madalin Giambasu (giambasu_at_biochim.ro)
Date: Mon Aug 30 2004 - 03:01:05 CDT

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.

Here is my input script:

Molecular dynamics script
 &cntrl
    imin=0
    nstlim=400000, ntt=3,gamma_ln=1,
    ntpr=50, pencut=0.1, ntwx = 50,
    ntwe =50,
    cut=16,
    vlimit=10,
    ntb=0,
    ntc=2, nmropt=1,
 &end
 constrain ca
 10
 search
 CA * M *
 find
 end
 end
 &ewald
  eedmeth=5
 &end
 &wt
   type='TEMP0', istep1=0, istep2=35000, value1=0.0, value2=100.0, /
 &wt
   type='TEMP0', istep1=35001, istep2=70000, value1=100.0, value2=200.0, /
 &wt
   type='TEMP0', istep1=70001, istep2=100000, value1=200.0, value2=300.0,
/
 &wt
   type='TEMP0', istep1=100001, istep2=400000, value1=300.0, value2=300.0,
/
 &wt
   type='END' /

**********************************
The output looks like this:
**********************************

--------------------------------------------------------------------------------
   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 = 50, ntrx = 1, ntwr =
500
     iwrap = 0, ntwx = 50, ntwv = 0, ntwe =
50
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0

Potential function:
     ntf = 1, ntb = 0, igb = 0, nsnb =
25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 16.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Molecular dynamics:
     nstlim = 400000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 10.00000

Langevin dynamics temperature regulation:
     ig = 71277
     temp0 = 300.00000, tempi = 0.00000, gamma_ln= 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 = 0.000 ps

           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
 TEMP0 0 35000 0.000000 100.000000 0 0
 TEMP0 35001 70000 100.000000 200.000000 0 0
 TEMP0 70001 100000 200.000000 300.000000 0 0
 TEMP0 100001 400000 300.000000 300.000000 0 0

 RESTRAINTS:
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

.................

******************************
The temperature evolution is :
******************************

NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
 NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 15.22 PRESS =
0.0
 NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 28.32 PRESS =
0.0
 NSTEP = 150 TIME(PS) = 0.150 TEMP(K) = 41.17 PRESS =
0.0
 NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 53.06 PRESS =
0.0
 NSTEP = 250 TIME(PS) = 0.250 TEMP(K) = 66.68 PRESS =
0.0
 NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 78.52 PRESS =
0.0
 NSTEP = 350 TIME(PS) = 0.350 TEMP(K) = 89.48 PRESS =
0.0
 NSTEP = 400 TIME(PS) = 0.400 TEMP(K) = 100.42 PRESS =
0.0

I hope you can help.

 
-------------------------------------------------------
Madalin G. Giambasu
Junior Research Assistant
Institute of Biochemistry of Romanian Academy of Science
Splaiul Independentei 296, 060031, Bucharest 17, Romania
Phone: (+4)021.223.90.69; FAX: (+4)021.223.90.68

-------------------------------------------------------

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