Dear David,
Thanks for your advice, I forgot the mailist fomer time.
I run the NPT simulation for 20ns, the density decreased from 0.8 to 0.03,
and pressure was around 19~21atm at last.
>From other mailist, such as NAMD, GMX, I reallized that this EPM2 model for
CO2 is a rigid model, which has no parameters for bond and angle, and works
well in MC simulation. And I manually give the bond constand of 2000
kcal/mol A^2 and angle constand 2000 kcal/mol theta^2 for MD simulation.
This would be the problem why I can not use EPM2. 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?
Thanks,
Liyang
2017-02-08 16:17 GMT-08:00 David Case <david.case.rutgers.edu>:
> On Wed, Feb 08, 2017, Liyang Zhu wrote:
>
> > Dear David,
>
> Please send amber-related questions to the mail reflector,
> amber.ambermd.org,
> and not to me personally. That way, many people can see your question and
> try
> to help, and the answers can help others with similar questions. See
> http://lists.ambermd.org/mailman/listinfo/amber for information on how to
> subscribe.
>
>
> >
> > The system is at 333 K and 20 atm (20 MPa), which is supercritical CO2
> with
> > a density of 0.8 g/ml.
> > Initially I tried gaff parameter, which gave a density of 1.2, that is to
> > high, so if some solutes were in the supercritical CO2, the diffusion
> would
> > be very slow. I also tried gaff2 parameter, which gave a better density
> of
> > around 0.95.
>
> It's not surprising that gaff/gaff2 do not give great performance for
> supercritical CO2, which is very far from the sort of molecules that were
> used
> in its parameterization.
>
> > I tried your suggestion, set ntb=2, ntp=1, pres0=20.0, taup=999999.0,
> > irest=1, ntx=5 (if ntx=7, the initial temperature is 0 K, not previously
> > heated 333 K). It shows that the pressure was at first as high as 900 atm
> > at 333K, and then decreased to 140 atm. During the pressure decreasing,
> the
> > temperature also decreased from 333 K to around 300 K, and then back to
> > 333K. So eventually it equilibrated at 140 atm, 333 K, with a initial
> > density of 0.5.
>
> Why not try a initial simulation using the experimental density? If you
> use a density of 0.5 under thermodynamic conditions where the denisty
> "should" be 0.8, you may be seing bubbles in your system, and it could
> be very hard to equilibrate. Using the experimental density will also
> allow you to gain confidence (or not) that you have transferred the EMP2
> potential function correctly to Amber. (I'm not at all familiar with this
> potential, but linear molecules can be tough to handle in cartesian codes.
> But work first to get a well equilibrated system.)
>
> [To be clear here: I'm suggested that you the volume (and hence the
> density) fixed, regulate the temperature to the value you want, make sure
> that you have reached equilibrium, and see what the average pressure is.]
>
> >
> > I noticed that most of the articles using EMP2 are for Monte Carlo
> > simulation, is it because the parameters of 12-6 LJ potential (EMP2) is
> not
> > transferable from Monte Carlo simulation to Molecular Dynamic simulation?
>
> No.
>
> ....good luck...dac
>
>
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Received on Thu Feb 09 2017 - 10:00:03 PST
