It is not clear what is wrong with your system without checking the things throroughly.
Therefore, 1) double-chack your topology. 2) submit longer MD simulation. 3) double-check the temperature which is requested in the MDP file. -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 On Tue, May 3, 2011 at 2:00 AM, Prema Awati <prem...@iiserpune.ac.in> wrote: > Sir, > > Thanks for your response !! > > The LJ parameters are defined in forcefield database so it need not > require to be mentioned in topology,I followed gromacs manual.But If its > working by adding then please guide me regarding LJ parameters. I used OPLS > forcefield to create raw topology and then edited referring Tsuzuki"s. > > Tsuzuki et.al used basically Lopes et.al forcefield which was > refined(partial charges,nonbonding parameters ) to reproduce experimental > density. > > I obtained 1.0045 g/cm3 density which is poor to do final production run in > order to study diffusive dynamics of ionic liquids, so I am looking to get > exact density that of Tsuzuki. > > Thanks. > >
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