AMBER Archive (2005)
Subject: AMBER: langevin, GB and simulated annealing - 2

From: pascal.baillod_at_epfl.ch
Date: Tue Apr 19 2005 - 16:07:23 CDT

Next message: David A. Case: "Re: AMBER: Non-Bonded Cutoff vs PME"
Previous message: Junmei Wang: "RE: AMBER: antechamber for cyano group"
In reply to: Carlos Simmerling: "Re: AMBER: langevin, GB and simulated annealing?"
Next in thread: David A. Case: "Re: AMBER: langevin, GB and simulated annealing - 2"
Reply: David A. Case: "Re: AMBER: langevin, GB and simulated annealing - 2"
Reply: Andreas Svrcek-Seiler: "Re: AMBER: langevin, GB and simulated annealing - 2"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

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

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

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