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