On Mon, 2014-02-24 at 16:56 +0000, Mele N. wrote:
> Thanks you for your answer.
>
> I applied what you told me:
>
> - first I tried to turn on shake during minimization but the minimization crash with the same error:
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
>
> - after this error I run a new minimization without shake and no problem.
>
> - So i modified my equilibration input file as we advice me with ntb=1 and ntp=0 :
>
> Equilibration
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=100, dt=0.001,
> ntc=2, ntf=2,
> ntb=1, ntp=0, taup=2.0,
> ntpr=1, ntwx=1, ntwr=1,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,iwrap=1,
> /
>
>
> and unfurtunally same error:
>
> vlimit exceeded for step 0; vmax = 54.5176
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 1 35579 45871 45873
>
> Note: This is usually a symptom of some dee
>
> Have you any iea what is wrong with my system ??
Did you look at the specified atoms to see what was happening at the end
of the heating stage?
>
>
> Many thanks,
>
> Regards,
>
> ________________________________________
> De : David A Case [case.biomaps.rutgers.edu]
> Envoyé : lundi 24 février 2014 12:54
> À : AMBER Mailing List
> Objet : Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished
>
> On Mon, Feb 24, 2014, Mele N. wrote:
> >
> > I am trying to equilibrate a box of mixture water DMSO/Water created thanks to packmol software. During the equilibration step I get this error:
> >
> > vlimit exceeded for step 0; vmax = 128.9242
> >
> > Equilibration
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > nstlim=100, dt=0.002,
> > ntc=2, ntf=2,
> > ntb=2, ntp=1, taup=2.0,
> > ntpr=1, ntwx=1, ntwr=1,
> > ntt=3, gamma_ln=2.0,
> > temp0=300.0,iwrap=1,
> > /
>
> Equilibrate first with ntb=1,npt=0, then move to ntb=2,ntp=1. Also, for
> some systems, doing a bit of equilibration with dt=0.001, before moving
> to dt=0.002 sometimes helps.
>
> The fact that you get the error at step 0 is odd. It might be good to re-do
> the minimization step with SHAKE turned on. Generally, you want the
> minimization and MD steps to use identical parameters.
>
> ...dac
>
>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Feb 24 2014 - 09:30:03 PST
