Hi, Hannes
Yes, I realized this. Thanks.
/ Samuel
2010/1/13 Hannes Kopitz <Hannes.Kopitz.gmx.de>:
> 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 - 04:30:03 PST
