Here is my input file.
&cntrl
imin = 0, irest = 1, iwrap=1 ,ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 308.0, temp0 = 308.0,
ntt = 1, gamma_ln = 0,
nstlim = 100000, dt = 0.002,
ntpr = 100, ntwx = 500, ntwr = 1000
----- Original Message -----
From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Thursday, June 17, 2010 1:09 pm
Subject: Re: [AMBER] problem with the energetics of the system
To: AMBER Mailing List <amber.ambermd.org>
> You will have to give more details. What are you attempting to
> do? Can
> you sends your input files?
>
> Gustavo.
>
> On Jun 17, 2010, at 12:05 AM, Homa Azizian wrote:
>
> > Hi amber users,
> > My jobs of simulation stop with this message in out file:
> > | Local SIZE OF NONBOND LIST = 1100282
> > | TOTAL SIZE OF NONBOND LIST = 35026002
> > vlimit exceeded for step 0; vmax = 388.4665
> > vlimit exceeded for step 1; vmax = 399.4700
> > vlimit exceeded for step 2; vmax = 387.9217
> > vlimit exceeded for step 3; vmax = 352.8459
> > vlimit exceeded for step 4; vmax = 32817.3873
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 3 302 606 607
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> >
> > I could not undrestad what happen to my system.
> > Thank you very much for replying.
> > Homa
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>
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Received on Wed Jun 16 2010 - 22:00:03 PDT
