Doing position-restrained simulation is useful to equilibrate solvent and ions.
If you would like to study the dynamics of the peptide, PRMD doesn't help. PRMD
is usually performed before production run for a duration from several hundred
ps to 1ns.
Regards,
Yang Ye
- Original Message
I understand.Thank you for the comparative analysis.
sarbani
On Tue, 23 Oct 2007 Mark Abraham wrote :
>sarbani chattopadhyay wrote:
>> yes , I had gone through the manual, but is that all? I mean to say that
>
sarbani chattopadhyay wrote:
yes , I had gone through the manual, but is that all? I mean to say
that even if the protein
suffers from high solvent forces (though the energy minimisation can be
done over the
whole system ie protein in solvated state) that may not pose much of a
problem , in c
yes , I had gone through the manual, but is that all? I mean to say that even
if the protein
suffers from high solvent forces (though the energy minimisation can be done
over the
whole system ie protein in solvated state) that may not pose much of a problem
, in case we
simulate for suffici
sarbani chattopadhyay wrote:
Hi,
I am new to the field of MD.I want to know what is the effectivity of
position restricted MD
ie. where is the advantage of doing Position restricted MD.I have a
small peptide of 3
reidues.Is it necessary to do a Position restricted MD. What difference
will i
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