Hi Tom,
1 ns sounds far too small to explore the various conformational states of a
protein of that size, and even worse if you expect the ligand to find it
lowest-energy conformation/position (unless you have placed it where it
binds). Perhaps you should consider enhanced sampling techniques like
Greetings all,
I am quite interested in this discussion, and wondered if some people would
like to add how they would assess the length their MD simulations. I am
currently simulating HIV-1 RT for 1 ns and seem to have very flat energy
profiles for almost anything (energy wise) I care to measure
Hey Widya,
In general, no, 15*2ns is not equal to 1*30ns. The reason for this lies in
correlation and relaxation times. 15 simulations of 2ns give good statistics
on relaxation and, if the system is equilibrated already, on short-term
processes. A single simulation of 30 ns may relax to equilibriu
Widya Desmarani wrote:
Dear gromacs user,
I have been trying to look for an answer for my following question from
our forum but still couldn't manage to find one. Probably it is trivial
but I am not sure.
Instead of running a single relatively long simulation (say for about 30
ns), is it
Dear gromacs user,
I have been trying to look for an answer for my following question from our
forum but still couldn't manage to find one. Probably it is trivial but I am
not sure.
Instead of running a single relatively long simulation (say for about 30
ns), is it acceptable if we simulate multi
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