Dear Mohd Athar, first of all that type of substance you indend to study? Is it organic or anorganic in nature? I was briefly checking the Information on the OPLS force field. If yo uhave all the data / Parameter for the elements and combination of elements it could work with MD provided it is also stable in a dynamic Simulation (sometimes static calculations work but dynamic do not). Following your description of the observations and Problems it is not clear to me if you refer to Problems of MD calculations that you carried out or something else. However Long distance interactions like ionic interactions can be treated in / by MD as Long as they are defined (properly) and the System is stable (enough) at the given temperature. Usually the ionic interactions reach much further than most of the MD models and the interactions with the not-modelled surrounding continuum (molecules in there) Need to be considered as well. This can be done by the Approach called Ewald sum (mation). However this may Need to be defined before as well as other Long-range interactions if they are not "automatically" integrated in the program or Software package you are using.

The reason why I was asking about organic or anorganic interactions (which relates also to so-called hard and soft interactions) is that I remember the work of some former colleagues of mine who intended to carry out more or less classical MD for modelling organic interactions and activities like ion Exchange in organic cells. A Long Story short, it didn't worked out at all. The hard interactions that we usually model and consider in MD were too strong and therefore nothing happed in the models in this case (at least not what was expected). The are surely more suitable modelling approaches for organic interactions available (like in the pharmaceutical field and in medical science). I guess the principles, General chemistry and physics are more or less the same, but the interactions will be different as they will Show higher probability. A reason for this I can imagine could be the effect of catalysis / catalysers.

Sorry I have no solution for your Problems (one would Need to look into the Details and carry out tests on all Levels to identify that devil, if it isn't a principle Problem. 

Ruediger

Dea Rüdiger Rentsch, let me first express sincere thanks for all the kind words/answer.

Actually, my question is related to MD simulation setup and as well as the system generation for it (as I dont know the error). Moreover, my anion is puerly inorganic in nature (halides, nitrates, thiocyanate) that can be anticipated to form purely ionic interactions. In MD modeling with OPLS_2005 foce field, even after taking care of the partial charge (kollman charge) of the ion (that was calculated at DFT level using gaussian package), the anion is getting separated out from the interaction range of the receptor in MD calculation (using Desmond package of DJ Shaw group).

Regarding the stability of the input MD structure, I can assure that the complex structure was quantum mechanically minimized at the DFT level. Therefore, in prinicple it should sample the anions in the vicinity of receptor at least for the starting cycles of MD. In contrast to it, it doesnot dispay anything like that

This is the reason I suspect that there is some problem with my MD setup or the selection of method (most probably with the parameterization of anions). I will be very grateful, if you extend some more comments on this issue.

Also, there are few published reports for the same like. http://pubs.acs.org/doi/ pdf/10.1021/jo9907437

http://pubs.acs.org/doi/pdf/10.1021/ja020318m

https://www.ncbi.nlm.nih.gov/pubmed/28140582

thanks