[gmx-users] radial distribution function

[Moeed]

On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul <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.


> -Justin
>
>  Best,
>> moeed
>>
>>
>> On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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
>>
>>    --     ==============================**__==========
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
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> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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