Re: [AMBER] EPM2 Force field for CO2

From: David Case <>
Date: Thu, 9 Feb 2017 16:09:03 -0500

On Thu, Feb 09, 2017, Liyang Zhu wrote:

> I run the NPT simulation for 20ns, the density decreased from 0.8 to 0.03,
> and pressure was around 19~21atm at last.

Were you using ntp=1 and taup=999999.? That should correspond to a constant
volume simulation, and the density will not change.

Also, did you solve all the original problems of converting the LJ simga
into Amber's Rmin/2? You results make it look like your molecules are way to

> Some software such as
> Gromacs has constrain diretive to define rigid molecule, so is there
> methods to define the rigid 180 degree angle and bond lengh in Amber16?

I don't think so. My first approach would be to try to trick Amber into
thinking that CO2 is a three-point water molecule. But that would require
a good familiarity with Amber, and might not work for a linear molecule.


AMBER mailing list
Received on Thu Feb 09 2017 - 13:30:03 PST
Custom Search