Dear JunJun,
I do not believe that it is possible to use Belly with constant pressure. It is likely disabled because it corrupts the virial and so prevents the barostat from working. It is also extremely unphysical and it is not obvious why you would want to do it. The concept of pressure when you have some atoms artificially constained is not well defined.
If you specifically want to keep part of your system fixed in a location then I think the best way to do this is to use restraints and set a reasonably high restraint force.
All the best
Ross
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of JunJun Liu
> Sent: Wednesday, December 06, 2006 15:23
> To: amber.scripps.edu
> Subject: AMBER: ibelly not work
>
> Dear all,
> I'm using AMBER8. I want to fix some atoms during MD, then I use
> ibelly=1. However I find those atoms cannot be fixed unless I change
> "ntb=2 ntp=1" to "ntb=1, ntp=0".
> Could you please give me some idea on how to fix atoms at
> constant
> pressure(ntb=2)?
>
> # Control section
> &cntrl
> nstlim=50000 , dt=0.002, ntx=1, irest=0, ntpr=500,
> ntwr=500,ntwx=500 ,
> tempi=10.0, temp0=298.15, dtemp=10.0, ntt=1, tautp=2.0, ig=2858,
> ntb=1, ntp=0,
> ntc=2, ntf=2,
> nrespa=1,
> cut = 10.0,
> ibelly=1,
> &end
> &ewald
> &end
> G1
> ATOM 1 1288
> END
> G2
> ATOM 1290 1290
> END
> G3
> ATOM 1302 1818
> END
> END
>
>
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Received on Fri Dec 08 2006 - 16:23:05 PST
