AMBER Archive (2004)

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

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Aug 30 2004 - 08:21:36 CDT

was the system equilibrated at lower T first? was it minimized?
can you send more of the output, up to the first few energy printouts?
then we can see what the initial energies are and how fast they go up.

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

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.
>
>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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