Hi Samuel,
There are two problems with the energy decomposition in your case.
The first is as Thomas said, the energy decomposition only works with ifsc set to 0 or 1, where a multisander job is run.
The second is that you should set idecomp to 2 instead of 4. I just realized that this is a mistake in the Amber10 manual on page 26, I apologize for this. Have a look at page 100 for a correct description of the use of idecomp within TI. In TI only a decomposition on the per-residue level is possible. A decomposition on the pairwise per-residue level is not allowed since the PME scheme for long range interactions is used which contains a sum of per-atom terms.
Hope I could help you.
Cheers!
Hannes
-------- Original-Nachricht --------
> Datum: Wed, 13 Jan 2010 11:02:28 +0100
> Von: Samuel Genheden <samuel.genheden.gmail.com>
> An: amber.ambermd.org
> Betreff: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints
> 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
>
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Received on Wed Jan 13 2010 - 04:00:02 PST
