[gmx-users] radial distribution function
lecielll at googlemail.com
Fri Sep 9 22:01:16 CEST 2011
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.
On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Moeed wrote:
>> Dear users,
>> I have created radial distribution function plot for Carbon atoms in a
>> system containing polymer chains. I see some little jumps between first and
>> second peak.
>> I need your help to comment on how this behavior can be justified (or if
>> the plot is wrong).
>> g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
> How long is the sampling? In the absence of -e and with -b being hidden
> from us for some unknown reason, it's hard to guess. I'd say your
> simulation just isn't fully converged, although for complex systems that can
> be a challenge anyway. Nothing unusual.
> 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
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