I have performed a simulation in which I wanted the molecule to be with
the bond lenghts kept fixed. So I have turned SHAKE on with NTC=3.
But during the simulation it keeps the bond lengths at values other than
the ones I have introduced with the initial inpcrd file. Why is this
happening?
Here is my mdin file:
# IMIN -> tipo de simulacao
# NTX, IREST -> nature and format of input
# NTWX, NTWV, NTWE, NTWR, NTPR -> nature ando format of output
# NTB -> Periodic boundary
# NSTLIM, NSCM -> MD run flags
# NTT, TEMP0, TAUTP -> Temperature regulation
# NTC -> Shake
# MAXCYC -> Energy minimization flags
dmaca zwiterionico isolado a temperatura ambiente (equilibracao)
&cntrl
IMIN=0, IREST=0, NTX=1,
NTWX=100, NTWV=100, NTWR=500,
NTWE=100, NTPR=100,
NSTLIM=20000,
NTB=0, NSCM=100,
NTC=3, NTF=3,
NTT=1, TEMP0=298.15, TAUTP=1.0,
IG=209,
&end
Here is my mdout file:
-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
| Thu Oct 23 20:21:58 2003
File Assignments:
| MDIN: md.in
| MDOUT: md.out
|INPCRD: dmacaz.crd
| PARM: dmacaz.top
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
# IMIN -> tipo de simulacao
# NTX, IREST -> nature and format of input
# NTWX, NTWV, NTWE, NTWR, NTPR -> nature ando format of output
# NTB -> Periodic boundary
# NSTLIM, NSCM -> MD run flags
# NTT, TEMP0, TAUTP -> Temperature regulation
# NTC -> Shake
# MAXCYC -> Energy minimization flags
dmaca zwiterionico isolado a temperatura ambiente (equilibracao)
&cntrl
IMIN=0, IREST=0, NTX=1,
NTWX=100, NTWV=100, NTWR=500,
NTWE=100, NTPR=100,
NSTLIM=20000,
NTB=0, NSCM=100,
NTC=3, NTF=3,
NTT=1, TEMP0=298.15, TAUTP=1.0,
IG=209,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| New format PARM file being parsed.
| Version = 1.000 Date = 10/23/03 Time = 15:22:28
NATOM = 26 NTYPES = 6 NBONH = 13 MBONA = 13
NTHETH = 26 MTHETA = 16 NPHIH = 41 MPHIA = 21
NHPARM = 0 NPARM = 0 NNB = 119 NRES = 1
NBONA = 13 NTHETA = 16 NPHIA = 21 NUMBND = 11
NUMANG = 16 NPTRA = 7 NATYP = 8 NPHB = 0
IFBOX = 0 NMXRS = 26 IFCAP = 0 NEXTRA = 0
| Memory Use Allocated Used
| Real 2000000 2916
| Hollerith 400000 159
| Integer 2000000 318475
| Max Nonbonded Pairs: 5400000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
DMA
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 100, ntwv = 100, ntwe =
100
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 3, ntb = 0, igb = 0, nsnb =
25
ipol = 0, gbsa = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 20000, nscm = 100, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Temperature regulation:
ig = 209, ntt = 1, vrand = 0
temp0 = 298.15000, tempi = 0.00000, heat = 0.00000
dtemp = 5.00000, tautp = 1.00000
SHAKE:
ntc = 3, jfastw = 0
tol = 0.00001
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
DMA
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = 0.00100000
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 204
| TOTAL SIZE OF NONBOND LIST = 204
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -18.6028 EKtot = 0.0000 EPtot = -18.6028
BOND = 0.0000 ANGLE = 5.2959 DIHED = 0.0002
1-4 NB = 7.5111 1-4 EEL = -22.0513 VDWAALS = 2.0251
EELEC = -11.3838 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 50.59 PRESS = 0.0
Etot = -12.8448 EKtot = 2.3121 EPtot = -15.1570
BOND = 0.0000 ANGLE = 5.5465 DIHED = 0.0004
1-4 NB = 8.4466 1-4 EEL = -22.2237 VDWAALS = 4.0328
EELEC = -10.9596 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 65.80 PRESS = 0.0
Etot = -11.9244 EKtot = 3.0074 EPtot = -14.9318
BOND = 0.0000 ANGLE = 6.7884 DIHED = 0.0009
1-4 NB = 8.0730 1-4 EEL = -21.5459 VDWAALS = 2.9420
EELEC = -11.1903 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 69.78 PRESS = 0.0
Etot = -11.0472 EKtot = 3.1895 EPtot = -14.2366
And so it goes.....
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Received on Thu Oct 23 2003 - 23:53:01 PDT
