I am trying to run a quench molecular dynamics on a molecule. This molecule consists of Cyclopentadienyl rings with Fe together with a (CH)2 chain. I am using Materials Studio 6.1 (Accelrys) version program package.
The problem is, when I click on the run bottom then it is showing "the dynamics can't integrate the equation of motion for a particle of zero (or small) mass". But if I cut the Cyclopentadienyl rings together with Fe then there is no problem. That means there is no problem with the rest of the (CH)2 chain.
Does anyone know where the problem is?
Hi, did you check that all your atoms were typed with the selected force field?? that means parameters for each atoms were set correctly ? maybe a problem with Fe atom !!Well I haven't used the new 6.1 version but should be same principle as 5.5.
Hi, there is no problem with the parameters for the atoms. I also think that the problem is due to Fe atom as there is no problem with the rest of the atoms. But I don't understand that why the zero (or small) mass is showing in the dialogue when I click on the run button for the MD dynamics.
Maybe , the problem come from a binding bond between Fe atom and (CH)2.
The problem that you are facing is that you have a cyclopentadienyl ring which has a dummy atom representing the Pi system. This is not recognised by Forcite or Discover as a valid particle for molecular dynamics because it has no mass associated with it and hence the program gives an error.
I think that it is pretty hard to study MD of organometallics using classical simulations techniques. I did a quick search for "organometallics" on
http://references.accelrys.com
This turned up many hits but publications were nearly all using DMol3. I guess you could potentially delete the Pi system and create bonds between the cyclopentadienyl fragment and the metal atom but I am not convinced this would give good results (picking a forcefield might be challenging!)
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