[gmx-users] General Question

[pawan raghav]

Dear GROMACS team members,

I have a general question about the GROMACS, actually I have used GROMACS
for the simulation of 59 amino acids domain part of the protein
containing within it. This domain lies in the position from 34-92 out of 239
residues, this loop having only 12 residues similarity whose does not found
any similarity in this region. I have an objective to predict the behaviour
of such a large loop flexibility. So my question is that at what level of
accuracy, the loop optimization and prediction would be correct. Is it
possible to predict the loop structure on the basis of simulation or can
predict the structure of unstructure loop of a protein? Please comment on
this because some people criticising MD simulations prediction. Can we
predict the folded loop of a protein by using simulation? if yes then tell
me about the analysis methods in gromacs for loop particularly. One more
question is about the "dt" that it can be possible to change the value of dt
in .mdp file instead of 0.002 ps to 0.003 if yes then what is the
significance of this and what is the efeect of this on simulation?
-- 
Pawan
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