Hello, Amber users
I want to perturb a benzene molecule (bound to a protein) into nothing
using the TI facilities of Amber 10. This is similar to the tutorial
but I want to perturb to nothing instead of phenol. At the same time I
want to use energy decomposition (idecomp=4) and to apply restraints
(nmropt=1) to the benzene molecule. To perturb to nothing I use the
option ifsc=2, as explained in the manual. But when I run sander it
stucks at a particular place in the initialization phase. I have tried
to set ifsc to 0, and then sander runs perfectly fine. By looking
through the sander code I have located the "stucking" to the
synchronize_dec routine in decomp.f. Sander enters this function, but
it never leaves it.
My simple question is: what does this function do? I realize that it
synchronize something with MPI, but what? How can I cure my problem?
I use Amber10 with all the latest bug fixes.
Best regards,
Samuel
My input:
&cntrl
irest=1,ntx=5,
nstlim=25000,dt=0.002,
temp0=300.0,ntt=3,gamma_ln=2.0,
ntc=2,ntf=1,
cut=8.0,
ntpr=500,ntwx=0,ntwv=0,ntwe=0,iwrap=1,
ntb=2,ntp=1,pres0=1.0,taup=1.0,
ipol=0,igb=0,
scnb=2.0,scee=1.2,
ntr=0,nmropt=1,
icfe=0, clambda=0.90,
ifsc=2,scmask=':BNZ',
crgmask=':BNZ',idecomp=4,
logdvdl=0,dvdl_norest=1
&end
&wt type='END' /
DISANG=ti_rest
Residues to do decomposition
RRES 1 162
RRES 163 163
RRES 164 7937
END
Residues to print
RES 1 162
RES 163 163
RES 164 7937
END
END
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 13 2010 - 02:30:02 PST
