Dear David,
I have used ntp=1 ant taup=99999.0, indeed the volume change was
neglect-able, while the pressure is much large than expected.
Conversion of LJ parameters into Amber parameters are correct, I found some
articles using NONBON parameters very close to my CO2.frcmod file as
follows. The bond and angle parameters are taken from gaff2.dat. Then
using packmol to get a box.pdb of desired density. And using tleap to
generate the prmtop and inpcrd files.
In history, there are many mail lists about rigid CO2 model. So may be
there is no flexible CO2 parameters existing now, only rigid CO2 models are
widely used, which bring continuously problem for some users of Amber,
Gromacs and other MD softwares.
A possible way to solve this problem may be optimizing the parameters based
on gaff2.dat (includes inter-molecule parameters), so could anyone give
some suggestions about the flowsheets to optimize parameters for MD
simulation, for those small but widely used molecules?
Regards,
Liyang
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/1379.html
http://archive.ambermd.org/200810/0166.html
http://comments.gmane.org/gmane.science.biology.gromacs.user/76394
CO2.frcmod
*************************************************************
remark goes here
MASS
X 12.01 0.360 ATTN, need revision
T1 16.00 0.434 ATTN, need revision
T2 16.00 0.434 ATTN, need revision
BOND
X -T1 794.98 1.160 ATTN, need revision
X -T2 794.98 1.160 ATTN, need revision
ANGLE
T1-X -T2 118.817 180.0 ATTN, need revision
DIHE
IMPROPER
NONBON
X 1.5473 0.0559 ATTN, need revision
T1 1.7020 0.1600 ATTN, need revision
T2 1.7020 0.1600 ATTN, need revision
**********************************************************************
tleap.in
****************************************************
CO2=loadmol2 CO2.mol2
box=loadpdb box.pdb
loadamberparams CO2.frcmod
setbox box "centers" 0.0
saveamberparm box box.prmtop box.inpcrd
2017-02-09 13:09 GMT-08:00 David Case <david.case.rutgers.edu>:
> 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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>
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Received on Thu Feb 09 2017 - 16:00:03 PST
