Dear Ross
Thanks a lot for your detailed explanations and quick reponse!
Yes, i found i mistakenly inverted the use of ibelly. Now it should be good
for what i want.
I have two more quick question:
1) Is there any input limit ( i.e. how many charaters i can write on the
file of *.in)?
i need to freeze a lot of atoms on several residues with ibelly?
2) Is ibelly more efficient in compuaton than ntr?
ibelly only zeors the force on the fixed atoms while for ntr, the
computations are still needed for the contraints.
Thanks again!
Jim
On 5/31/10, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Hi Jim,
>
> Belly is back to front with respect to restraints. In belly you select the
> atoms that you want to allow to move. Thus if you just invert your
> selection
> you should be good.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of Jim Miller
> > Sent: Sunday, May 30, 2010 10:25 AM
> > To: amber.ambermd.org
> > Subject: [AMBER] Defunction of ibelly in Sander
> >
> > 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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>
>
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Received on Sun May 30 2010 - 21:00:05 PDT
