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 - 09:47:55 CDT

 The problem is that the evolution of the tenperature is wanted in such a
way to slowly
heat the system . Look at the same job output, but done with Beredensen
Thermostat,there are real differences: the LANGEVIN thermostat appears to
rise the temperature to 300K after 2ps, though it is said to raise it
after 70ps.

Here is the temperature evolution for NTT=1, Beredensen Thermostat:

NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
 NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 0.12 PRESS =
0.0
 NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 0.12 PRESS =
0.0
 NSTEP = 150 TIME(PS) = 0.150 TEMP(K) = 0.14 PRESS =
0.0
 NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 0.14 PRESS =
0.0
 NSTEP = 250 TIME(PS) = 0.250 TEMP(K) = 0.15 PRESS =
0.0
 NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 0.14 PRESS =
0.0
 NSTEP = 350 TIME(PS) = 0.350 TEMP(K) = 0.14 PRESS =
0.0
 NSTEP = 400 TIME(PS) = 0.400 TEMP(K) = 0.13 PRESS =
0.0

Here is the temperature evolution for NTT=3, Langevin Thermostat:

 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

On Mon, 30 Aug 2004, Carlos Simmerling wrote:

> did you want to restrain the CA atoms? there is a group restraint listed
> but you didn't use ntr=1 so it is ignored. if you use them, 10 might be
> too large
> for a force constant, try 1.0 if you have trouble.
> otherwise I don't see a problem but maybe someone who uses LD for
> temperature ramping may spot something.
>
> ===================================================================
> 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:
>
> >
> >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
> >
> >File Assignments:
> >| MDIN: heat+eqln.inp
> >| MDOUT: mdout
> >|INPCRD: x_na1.rst
> >| PARM: x_na.prmtop
> >|RESTRT: x_na2_lent_ca.rst
> >| REFC: x_na1.rst
> >| MDVEL: mdvel
> >| MDEN: mden
> >| MDCRD: mdcrd
> >|MDINFO: mdinfo
> >|INPDIP: inpdip
> >|RSTDIP: rstdip
> >
> >
> > 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
> >
> >
> >| Memory Use Allocated
> >| Real 415754
> >| Hollerith 38256
> >| Integer 1455716
> >| Max Pairs 12254976
> >| Max Rstack 113040
> >| Max Istack 31520
> >| Total 57961 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 = 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
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> > NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 15.22 PRESS =
> >0.0
> > Etot = -3304.0423 EKtot = 239.8629 EPtot =
> >-3543.9052
> > BOND = 206.7875 ANGLE = 1054.7072 DIHED =
> >3959.0853
> > 1-4 NB = 1289.0443 1-4 EEL = 6367.8200 VDWAALS =
> >-2479.8637
> > EELEC = -13941.4858 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> > NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 28.32 PRESS =
> >0.0
> > Etot = -2859.1804 EKtot = 446.3120 EPtot =
> >-3305.4924
> > BOND = 255.9120 ANGLE = 1172.4957 DIHED =
> >3979.4847
> > 1-4 NB = 1289.9858 1-4 EEL = 6363.3274 VDWAALS =
> >-2481.6255
> > EELEC = -13885.0725 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> > NSTEP = 150 TIME(PS) = 0.150 TEMP(K) = 41.17 PRESS =
> >0.0
> > Etot = -2465.8044 EKtot = 648.7614 EPtot =
> >-3114.5659
> > BOND = 302.9045 ANGLE = 1277.1544 DIHED =
> >4016.1194
> > 1-4 NB = 1293.2318 1-4 EEL = 6365.1019 VDWAALS =
> >-2467.1688
> > EELEC = -13901.9090 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> > NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 53.06 PRESS =
> >0.0
> > Etot = -2085.7407 EKtot = 836.0203 EPtot =
> >-2921.7610
> > BOND = 353.6672 ANGLE = 1361.9579 DIHED =
> >4046.4720
> > 1-4 NB = 1293.5304 1-4 EEL = 6369.6712 VDWAALS =
> >-2434.4922
> > EELEC = -13912.5674 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> > NSTEP = 250 TIME(PS) = 0.250 TEMP(K) = 66.68 PRESS =
> >0.0
> > Etot = -1695.4135 EKtot = 1050.6658 EPtot =
> >-2746.0793
> > BOND = 380.6981 ANGLE = 1452.2613 DIHED =
> >4059.9768
> > 1-4 NB = 1312.0277 1-4 EEL = 6366.0306 VDWAALS =
> >-2461.5100
> > EELEC = -13855.5637 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> > NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 78.52 PRESS =
> >0.0
> > Etot = -1300.9163 EKtot = 1237.3369 EPtot =
> >-2538.2532
> > BOND = 434.9664 ANGLE = 1567.9427 DIHED =
> >4093.2816
> > 1-4 NB = 1306.9961 1-4 EEL = 6360.8800 VDWAALS =
> >-2460.6108
> > EELEC = -13841.7092 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> > NSTEP = 350 TIME(PS) = 0.350 TEMP(K) = 89.48 PRESS =
> >0.0
> > Etot = -919.6005 EKtot = 1410.0507 EPtot =
> >-2329.6513
> > BOND = 474.8886 ANGLE = 1643.6900 DIHED =
> >4120.2951
> > 1-4 NB = 1319.6168 1-4 EEL = 6367.5290 VDWAALS =
> >-2449.8313
> > EELEC = -13805.8394 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> > NSTEP = 400 TIME(PS) = 0.400 TEMP(K) = 100.42 PRESS =
> >0.0
> > Etot = -596.9411 EKtot = 1582.3260 EPtot =
> >-2179.2671
> > BOND = 493.7875 ANGLE = 1722.6750 DIHED =
> >4124.0786
> > 1-4 NB = 1325.3619 1-4 EEL = 6382.6767 VDWAALS =
> >-2434.9758
> > EELEC = -13792.8710 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> >
> >------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >===============================================================================
> >
> >
> >-------------------------------------------------------
> >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
> >
> >-------------------------------------------------------
> >
> >
> >-----------------------------------------------------------------------
> >The AMBER Mail Reflector
> >To post, send mail to amber_at_scripps.edu
> >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu