AMBER Archive (2004)

Subject: Re: AMBER: Amber8: Vlimit problem again

From: Yuhui Cheng (amberuser3_at_yahoo.com)
Date: Wed Jul 21 2004 - 18:44:09 CDT

Dear David & German,
     Thank you for your response. I set dt=0.001 as
you suggested. And my system sucessfully lasted 300 ps
and then the output reports the vmax exceeded the
default vlimit again.
     Can I turn off shake and set dt=0.0005? Actually,

my simulation system should be instable since it's the
product complex and the phosphorylated peptide should
be released. Is it possible that the high fluctuation
of the product peptide results in such a problem?

Thanks a lot,
Yuhui
   
--- "David A. Case" <case_at_scripps.edu> wrote:
> On Thu, Jul 15, 2004, Yuhui Cheng wrote:
>
> > " vlimit exceeded for step 25175 ; vmax =
> 88.8293391220360
>
> See what behavior you get with dt=0.001 instead of
> 0.002. Increasing
> vlimit is not going to help you any, in all
> likelihood.
>
> ...good luck...dac
>
>
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