Dear Amber Users
I want to *totally* fix the protein atoms in water (TIP3P) in NVT.
I used ibelly in *.in file. Why ibelly can not work to fix the atoms i
selected.
I saw the change of DIHED and coordinates.
Can any one help with the reason and suggest a way to frozen the atoms
positions that i want?
Thanks!
This is my *.in file
--------------------------------------
300-300K constant temp, v MD
&cntrl
imin=0,
ntb=1,ntt=1,
cut=18.0,
ntc=2, ntf=2,
tempi=300.0, temp0=300.0,
iwrap=1,
nstlim=100000, dt=0.001,
ntpr=500, ntwx=2000,
ibelly=1
/
Hold lyszyme fixed
RES 1 129
END
END
------------------------------
Although i can see this on the file of *.out
ibelly looks to work, but i still see change of DIHED.
I am using TIP3P water. if the protein is fixed, why
DIHED is changed.
-------------------------------------------------------------------
LOADING THE BELLY ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
Hold lyszyme fixed
GRP 1 RES 1 TO 129
Number of atoms in this group = 1968
----- END OF GROUP READ -----
.....
------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 77.000 TEMP(K) = 296.99 PRESS =
0.0
Etot = -870245.3768 EKtot = 1456.8415 EPtot =
-871702.2183
BOND = 392.8048 ANGLE = 933.9711 DIHED =
1375.8667
1-4 NB = 452.1472 1-4 EEL = 3940.6898 VDWAALS =
-1483.0180
EELEC = -877314.6799 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.9858E+00
------------------------------------------------------------------------------
NSTEP = 1500 TIME(PS) = 77.500 TEMP(K) = 299.35 PRESS =
0.0
Etot = -870248.6313 EKtot = 1468.4374 EPtot =
-871717.0687
BOND = 364.1676 ANGLE = 918.9277 DIHED =
1359.8530
1-4 NB = 465.4926 1-4 EEL = 3959.8302 VDWAALS =
-1468.0510
EELEC = -877317.2889 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.9858E+00
-----------------------------------------------------------------------------
Compared with input and out coordinates, the coordinates of the atoms which
are fixed with ibelly, still change with timesteps.
Copied from the input *.rst file
44.0391554 33.0419701 57.6206021 44.6241079 32.5355513 58.2698121
44.1731203 34.0119251 57.8682736 43.1051938 32.7022890 57.8006923
44.4098863 32.7431512 56.2579664 44.4705971 31.6549606 56.2739489
Copied from the output *.rst file
44.1438086 32.9139750 57.5409065 44.9432768 32.8378522 58.1534078
43.7911372 33.8511145 57.6731659 43.4404119 32.2880863 57.9064148
44.5645991 32.6420854 56.1582065 44.9799746 31.6369641 56.0854166
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Received on Sun May 30 2010 - 10:30:04 PDT
