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
big....
> 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.
....dac
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Received on Thu Feb 09 2017 - 13:30:03 PST
