On Tue, Jun 18, 2013, Bailey, Steven wrote:
>
> Setting up a complex of a number of PEG chain linked units I then run
> antechamber to obtain charges and input files.
> The MD simulation uses igb=1.
> After equilibrating to 300K I examine the MD output and the molecules
> show no interaction i.e. they seem to be frozen with no twisting
> and no vdW nor charge interactions. When running using a Dreiding
> force field for example in other MD packages there is a great deal of
> interaction. Can anyone advise what might be going wrong or would this
> be expected using the Gaff force field.
Are you sure the only difference between the two simulations (GAFF vs
Dreiding) is the force field? The qualitative behavior of MD should be the
same. Did you run both calculations in the same program, with the same
settings? It is very hard to get much insight from your short description,
but it sounds more like a thermostat problem than a force field problem.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 18 2013 - 07:00:04 PDT
