you don't really give us enough information.
what do you mean by "on protonated proteins"? how did you build these? how
was the equilibration done? how long into REMD before it crashed?
On Fri, Oct 15, 2010 at 2:24 AM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> I had a REMD job running fine with following input:
>
> REMD
> &cntrl
> irest=1, ntx=5,
> nstlim=1000000, dt=0.002,
> ntt=3, gamma_ln=2.0,
> temp0=320.0, ig=9665,
> ntc=2, ntf=2, nscm=1000,
> ntb=0, igb=5,
> cut=16, rgbmax=16, saltcon=0.2, gbsa=1,
> ntpr=500, ntwx=500, ntwe=500,
> nmropt=1,
> numexchg=1000,
> /
> &wt TYPE='END'
> /
> DISANG=uhprp_chir.dat
>
> With the sme input parameters, but worked on protonated proteins, I got
> following problem:
>
> ========================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
>
> The job stopped for exceeded velocity.
> What shall I do to get the problem solved?
> Thanks for the help!
>
> Sophia
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Received on Fri Oct 15 2010 - 04:00:02 PDT
