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 - 01:30:03 PST
