AMBER Archive (2004)
Subject: Re: AMBER: temperature scaling with ntt=3(Langevin thermostat)

From: Madalin Giambasu (giambasu_at_biochim.ro)
Date: Mon Aug 30 2004 - 08:51:35 CDT

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This are the first steps of the simulation. I killed this job, but I can
provide , if there is need, a longer output.

         -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 08/30/2004 at 10:18:44
[-O]verwriting output

Here is the input file:

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' /

--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 66.526
| New format PARM file being parsed.
| Version = 1.000 Date = 08/24/04 Time = 11:43:08
NATOM = 6304 NTYPES = 15 NBONH = 3047 MBONA = 3330
NTHETH = 7062 MTHETA = 4535 NPHIH = 13354 MPHIA = 9745
NHPARM = 0 NPARM = 0 NNB = 35072 NRES = 430
NBONA = 3330 NTHETA = 4535 NPHIA = 9745 NUMBND = 43
NUMANG = 93 NPTRA = 49 NATYP = 30 NPHB = 0
IFBOX = 0 NMXRS = 24 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 = 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

Number of triangulated 3-point waters found: 0

Sum of charges from parm topology file = -0.00000047
Forcing neutrality...

--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------

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

eedmeth=5: Using 1/r dielectric

---------------------------------------------------
| Local SIZE OF NONBOND LIST = 3224429
| TOTAL SIZE OF NONBOND LIST = 3224429

NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -3810.6919 EKtot = 0.0000 EPtot =
-3810.6919
BOND = 218.8366 ANGLE = 951.6952 DIHED =
3936.4964
1-4 NB = 1276.1936 1-4 EEL = 6371.2105 VDWAALS =
-2448.1057
EELEC = -14117.0186 EHBOND = 0.0000 RESTRAINT =
0.0000

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