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 ??
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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Received on Mon Feb 24 2014 - 09:00:08 PST
