Hi Sophia,
From the output you pasted, it looks as though your job has died at
the first step of (REMD) dynamics -- is this correct? If so, what
sort of minimization and equilibration have you done before starting
the replica exchange? The reason I ask is that your potential energy
is nearly +4000 kcal/mol, which *might* indicate that there are some
bad contacts, etc. (Though positive potential energies do not always
mean that there is something wrong.) This in turn may suggest that
you need to do more minimization and/or equilibration before starting
the exchange portion of the simulation...
Best,
Paul
On Oct 8, 2010, at 9:50 PM, Cheng-I Lee wrote:
> Hi,
>
> I've run a job of replica -exchange molecular dynamics with 24
> replica.
> However, the calculation was stopped with following message. Could
> anyone
> help me to solve this problem?
>
> Thanks a lot!
>
> Sophia
>
>> From remd.mdout:
>
> 4. RESULTS
> --------------------------------------------------------------------------------
> REMD: Initializing remlog.
> REMD: Getting initial energy for replica 1
> | # of SOLUTE degrees of freedom (RNDFP): 4302.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 4302. NUM_NOSHAKE = 0 CORRECTED RNDFP
> = 4302.
> | TOTAL # of degrees of freedom (RNDF) = 4302.
> REMD: Exiting runmd after getting initial energies for replica 1
> REMD: myEptot= 3993.7832 myTargetTemp= 320.00 mytemp= 0.00
> ==========================REMD EXCHANGE
> CALCULATION==========================
> Exch= 1 RREMD= 0
> Replica Temp= 320.00 Indx= 1 Rep#= 1 EPot= 3993.78
> Partner Temp= 370.00 Indx= 24 Rep#= 24 EPot= 4311.51
> Not controlling exchange.
> Rand= 0.184210E+00 MyScaling= -1.00 Success= F
> ========================END REMD EXCHANGE
> CALCULATION========================
> REMD: checking to see if bath T has changed: 320.00->320.00
> | # of SOLUTE degrees of freedom (RNDFP): 4302.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 4302. NUM_NOSHAKE = 0 CORRECTED RNDFP
> = 4302.
> | TOTAL # of degrees of freedom (RNDF) = 4302.
> vlimit exceeded for step 0; vmax = 20.5344
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Received on Fri Oct 08 2010 - 22:30:03 PDT
