Molecular dynamics simulation

[alpha2cen]

Ideal gas law is simple and very useful for calculation of high temperature thin gas phase.

To calculate real gas, one of simple simulation methods is molecular dynamics(MD) simulation.

How to simulate very simple real gas phase? Can we do simple simulation at the PC?

[timo]

- What the PC? Did you mean the CP, the critical point?

- The simplest way is to take one of the mainstream programs, plug in your system (or even take a setup you found on the net), and let the simulation run.

- You might want to look at this lecture notes. The first tutorial is the simulation of the condensation of an argon gas in gromacs. Playing with the parameters should be relatively easy, the steps are all given and the required setup files should all be provided.

- The alternative is of course writing your own program. That's also rather easy (we're talking about "F=ma"-physics, after all), but I imagine in can become very typing-intensive and boring at some point.

[alpha2cen]

- What the PC? Did you mean the CP, the critical point?

- The simplest way is to take one of the mainstream programs, plug in your system (or even take a setup you found on the net), and let the simulation run.

- You might want to look at this lecture notes. The first tutorial is the simulation of the condensation of an argon gas in gromacs. Playing with the parameters should be relatively easy, the steps are all given and the required setup files should all be provided.

- The alternative is of course writing your own program. That's also rather easy (we're talking about "F=ma"-physics, after all), but I imagine in can become very typing-intensive and boring at some point.

Thank you for good answer. I would like to calculate simple argon pressure slightly above the boiling point by using MD method. Edited February 18, 2011 by alpha2cen

[timo]

I would think that a simulation equilibrating a few hundred argon atoms can be easily done on a personal computer within a few minutes. So if you're only interested in the pressure of the system, the I don't see a huge problem. Keep in mind that the results for a few hundred atoms can differ from that of [math]10^{23}[/math] atoms, though!

[Mariana]

Hello!

 

I'm running a molecular dynamics of a protein, with periodic boundary conditions (my box of water), and the program NAMD.

 

What I want to do is equilibrate my system first, by combining minimization and equilibration steps, so... in order to do that, when i take the last structure of my system, previously equilibrated at 1 atm and 300 K (with a value of "constrain" = 16 in backbone) and want to keep doing the equilibrium stage -now with a value of "constrain" = 14 to go gradually releasing restrictions in the backbone- and to not lose my protein secondary structure, from the beginning of the calculation it falls, warning that the simulation is unstable because the atoms have more speed than originally permitted.

 

What do you recommend me in terms of the dynamic protocol to meet my goal?

 

Thanks in advance,

 

best regards from Venezuela.

[biki]

Hi,

Is it necessary to include Ewald summation if we want to calculate the electrostatic force between atoms from a molecular dynamics trajectory. I mean I know that Ewald sum or any other such algorithm is mandatory to generate the MD trajectory itself. But I want to calculate it from a given trajectory.

 

 

thanks,

Regards,

Biki

[phamdinhquochuy]

Hello

 

I am using Gaussian to derive force field parameters (force constants) for a metal site, and gaussian out put file contains the Hessian matrix.

Any one know a tools or a script to convert this Hessian matrix to force constants?

 

Than you in advanced,

And best regards,

 

Pham