________________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : lundi 24 février 2014 17:10
À : amber.ambermd.org
Objet : Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished
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?
THe problem is I can' t see anything because I don' t get any output file. The mdcrd that I get at the end is empty.
I can't pass any step during the heating.
>
>
> 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 - 09:30:04 PST
