Re: [AMBER] problem running MD for diphosphoric acid anion

From: necmettin pirinccioglu <pirincn.gmail.com>
Date: Mon, 29 Feb 2016 09:56:44 +0200

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. best wishes, necmettin
-- 
Necmettin Pirinccioglu (BSc, PhD)
Department of Chemistry
University of Dicle
21280 Diyarbakir
TURKEY



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Received on Mon Feb 29 2016 - 00:00:03 PST
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