[gmx-users] radial distribution function

[Justin A. Lemkul]

Moeed wrote:
> 
> 
> On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Moeed wrote:
> 
>         Thank you Justin for your reply. Simulation is 5 ns long (
>         before this a 500 ps NVT was done as equilibration) and total
>         energy has been equilibrated after around 3 ns.
> 
>          -b is set to 4000 that is the last 1 ns has been used for rdf.
> 
> 
>     For all but the simplest systems this simulation length and data
>     analysis period is insufficient.  How big is your polymer?  Proper
>     sampling may take tens to hundreds of ns of data collection.
> 
> Thanks. There are about 250 backbone carbons on 4 chains. Molecular 
> weight of each chains is around 3700 g/mol. I have been looking at total 
> energies and densities to equilibrate by checking sign change of 
> Tot-Drift for these properties before 5 ns. I actually dont see a big 
> change in energies. Is there any criteria to check on this using RMSD or 
> error? (so far I have been using sing change of Tot-Drift).
> 
> Please guide me. Thank you.
>  

The criteria should be whatever experimental observables you wish to reproduce. 
  Once those have converged to reliable values, you've done enough simulation. 
Total energy should always remain (relatively) constant throughout a simulation; 
it is a relatively insensitive measure for assessing equilibrium.

Even simple, robust protein systems are not reliably converged in 5 ns.  I 
sincerely doubt that large polymer chains are either, especially with the 
possibility of entanglement or configurational changes.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================