[gmx-users] simulation_time

[Tsjerk Wassenaar]

Hi Nikita,

That's actually a good question, and I think it hasn't been phrased like
this before. I rephrase it slightly again, so it says "which parameters
should be considered part of a force field?"

The first thing that springs to mind is not really a parameter, but a vital
part of the force field: the solvent model. pdb2gmx has a list of water
models of choice for each force field, although some force fields have
several water models, which were then developed to match, but possibly
tailored to specific goals.

The simulation parameters are those related to (non)bonded interactions,
temperature and pressure coupling, of which the latter two are less
critical. However, things like the coupling constants (tau_t/tau_p) may
affect the properties of the system, and for sure force fields have limited
temperature and pressure ranges within which the physics is acceptable.

The trickiest are the non-bonded interactions, where care always needs to
be taken, as these are intimately linked to core parameters of the force
field: the partial charges on atoms and the non-bonded parameters. In
particular, consider the following settings integral part of the force
field:

coulombtype
coulomb-modifier
rcoulomb
rcoulomb-switch
epsilon-r
epsilon-rf

vdwtype
vdw-modifier
rvdw
rvdw-switch
DispCorr

---

Hope it helps,

Tsjerk









On Wed, May 18, 2016 at 9:20 AM, Ms. Nikita Bora <niki24 at tezu.ernet.in>
wrote:

> Thank you sir for the reply...
>
> a few queries are still there....
>
> 1) what are the parameters that change according to force fields??
> 2) and what are the minimum cut offs for the parameters that changes
> according to force fields or is there any link where the information can
> be retrieved.
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.