temperature for MD of a protein
Hi,
thanks for all the replies to my previous question. I resolved the issue
with abrormal bond energies.
I have a question regarding the temperature at which MD needs to run for a
protein. I am new to PDB files, so this might be a trivial question. The
starting coordinates to simulate a protein are taken from the PDB.
1.How does one decide at what temperature the MD run needs to be done?
2.In other words, experimentally, when a PDB structure is determined, is
temperature a relevant factor?
3. would the structure be different if done at a different temperature?
4. is the temperature information encoded in the PDB file?
Thanks
vani