Hey,
Smaller time step may help.
On Mar 3, 2016 2:52 PM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
> Do you have a successful run previously where you warmed up your system
> to 600K? I would try setting ntpr and ntwx to 1 and look at the result.
> Apparently the bond between atoms 1 and 2 is being stressed too much.
> You may need a shorter time step for such a high temperature.
>
> Bill
>
> On 3/3/16 12:49 AM, necmettin pirinccioglu wrote:
> > ---------- Forwarded message ----------
> > From: necmettin pirinccioglu <pirincn.gmail.com>
> > Date: Mon, Feb 29, 2016 at 9:56 AM
> > Subject: Re: problem running MD for diphosphoric acid anion
> > To: AMBER Mailing List <AMBER.ambermd.org>
> >
> >
> >
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> >
> > Dear All,
> > I have been running MD for diphosphoric acid anion with the following
> input
> > but I get the error message below. Helps will be welcomed!
> >
> > INPUT
> > &cntrl
> > imin=0, irest=1, ntx=5,
> > nstlim=250000, dt=0.002,
> > ntc=4, ntf=4,
> > ntt=1, tautp=0.5,
> > tempi=600.0, temp0=600.0,
> > ntpr=500, ntwx=500,
> > ntb=0, igb=0,
> > cut=999
> > /
> >
> > ERROR MESSAGE!!!
> > ---------------------------------------------------
> > | Local SIZE OF NONBOND LIST = 1
> > | TOTAL SIZE OF NONBOND LIST = 1
> > vlimit exceeded for step 369; vmax = 22.0998
> > vlimit exceeded for step 373; vmax = 54.3352
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 0 1 1 2
> >
> > --
> > Necmettin Pirinccioglu (BSc, PhD)
> > Department of Chemistry
> > University of Dicle
> > 21280 Diyarbakir
> > TURKEY
> >
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Thu, 25 Feb 2016 01:00:15 -0800
> > From: Ross Walker <ross.rosswalker.co.uk>
> > Subject: Re: [AMBER] problem running MD for diphosphoric acid anion
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk>
> > Content-Type: text/plain; charset=us-ascii
> >
> > Hi Necmettin,
> >
> > A few notes here. Firstly it is best to run a small number of steps say
> > nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is
> > going wrong and visualize the trajectory.
> >
> > Also, tempi=600 is hot - that may causes issues - especially if your
> system
> > is not well equilibrated first.
> >
> > Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable
> > potential function. I would not recommend going above ntf=2,ntc=2 for
> > anything other than debugging.
> >
> > If changing to ntc=2,ntf=2 does not fix things then look carefully at
> your
> > structure - it may not be well enough minimized, it may have structural
> > deficiencies etc. Visualizing for and ntwx=1 run will help here.
> >
> > The parameters may also be suspect since this is not a regular amino /
> > nucleic acid - where did you get the parameters from?
> >
> > All the best
> > Ross
> >
> > Dear Ross, thanks for your kind reply. well firstly i did try with
> > ntf=2,ntc=2 (the number 4 is for my last try) and secondly i have
> employed
> > a shorter period. the trajectories indicate that the structure collapses
> > and the mds are ended with the error after a while. please find the md
> > trajectories as attached. I have done these calculations even at 700 K
> but
> > it worked fine with other small molecules. but i have just got this with
> > phosphoric acid. GAFF parameters were applied for the calculations...
> best
> > wishes, necmettin
> >
> >
> >
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Received on Thu Mar 03 2016 - 03:30:03 PST
