Dear All,
I am new AMBER10 user. As far as I could understand the manual, and
tutorial, I prepared one RNA system for doing MD simulations with TIP3P
water. When I am trying to minimize the system, the minimization stops
after steepest descent only, and not going further for conjugate gradient.
The calculation stops abruptly. Moreover when I use SHAKE, it gives LINMIN
failure, but when I dont use SHAKE, it gives EEL and EAMBER as ********.
The input file I took as:
input for minimization with restraints
&cntrl
imin = 1,
ntmin = 1,
dx0 = 0.02,
maxcyc = 15000,
ncyc = 7000,
ntpr = 100,
ntwr = 100,
ntwx = 100,
ntwv = 100,
ntwe = 100,
cut = 12,
iwrap = 1,
ntt = 3,
ntr = 1,
ntb = 1,
ntc = 1,
/
&ewald
ew_type = 0, verbose =0,
order = 4
/
Hold the RNA fixed
500.0
RES 1 162
END
END
And the output file is:
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 37.922
| New format PARM file being parsed.
| Version = 1.000 Date = 09/11/08 Time = 21:19:04
NATOM = 64295 NTYPES = 19 NBONH = 60646 MBONA = 3905
NTHETH = 4033 MTHETA = 6093 NPHIH = 8994 MPHIA = 11075
NHPARM = 0 NPARM = 0 NNB = 108007 NRES = 19951
NBONA = 3905 NTHETA = 6093 NPHIA = 11075 NUMBND = 45
NUMANG = 88 NPTRA = 41 NATYP = 31 NPHB = 1
IFBOX = 1 NMXRS = 34 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 4199389
| Hollerith 405723
| Integer 1806687
| Max Pairs 58808493
| nblistReal 771540
| nblist Int 2197918
| Total 285783 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
-------------------------------------------------------------------------------
eneral flags:
imin = 1, 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 =
100
iwrap = 1, ntwx = 100, ntwv = 100, ntwe =
100
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 15000, ncyc = 7000, ntmin = 1
dx0 = 0.02000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 103.434 Box Y = 75.845 Box Z = 104.570
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 108 NFFT2 = 75 NFFT3 = 108
Cutoff= 12.000 Tol =0.100E-04
Ewald Coefficient = 0.22664
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Hold the RNA fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
GRP 1 RES 1 TO 162
Number of atoms in this group = 5250
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 19628
Sum of charges from parm topology file = -0.00000014
Forcing neutrality...
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3146E-14 at 2.553520
| CHECK d/dx switch(x): max rel err = 0.7933E-11 at 2.712040
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 29724073
| TOTAL SIZE OF NONBOND LIST = 29724073
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -2.5691E+04 4.7469E+03 1.0290E+06 O 47646
BOND = 185.0610 ANGLE = 6320.6711 DIHED =
3600.1754
VDWAALS = 144433.7532 EEL = -165420.7272 HBOND =
0.0000
1-4 VDW = 3364.2477 1-4 EEL = -18174.1796 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -3.5619E+06 2.3706E+08 6.4100E+10 H2 31370
BOND = 14633.5684 ANGLE = 5112.5799 DIHED =
3723.1738
VDWAALS = 20229.8168 EEL = -3607696.2833 HBOND =
0.0000
1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT =
18115.3132
EAMBER = -3580011.2945
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -3.3009E+07 2.9205E+10 7.8970E+12 O 31419
BOND = 14633.5684 ANGLE = 5112.5799 DIHED =
3723.1738
VDWAALS = 20229.8162 EEL = ************* HBOND =
0.0000
1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT =
18115.3132
EAMBER = *************
------------------------------
-------------------------------- and so on the calc to 7000.
NSTEP ENERGY RMS GMAX NAME NUMBER
6900 -3.1597E+07 2.6711E+10 7.2226E+12 O 31419
BOND = 14633.5684 ANGLE = 5112.5799 DIHED =
3723.1738
VDWAALS = 20229.8162 EEL = ************* HBOND =
0.0000
1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT =
18115.3132
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
7000 -1.1928E+07 3.5494E+09 9.5976E+11 H2 31370
BOND = 14633.5684 ANGLE = 5112.5799 DIHED =
3723.1738
VDWAALS = 20229.8164 EEL = ************* HBOND =
0.0000
1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT =
18115.3132
EAMBER = *************
and here the calculation stops. I am missing something. But
can't figure out what. If anyone can please help me out..
Thanking you,
Regards,
Monika
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Received on Wed Sep 17 2008 - 03:08:10 PDT
