From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Wed Jun 22 2005 - 12:12:48 CDT
Yes adrian, the temperature coupling issue is interesting. I remember
in GROMACS you could use different coupling baths for solute and
solvent, to account for diffent Cp of both, nevertheless in NAMD at
laest I have not seen a way to do the same. As in Daggett's papers
they show unfolding of CI2 could be reached rearly in ~225 ps at 498K
in NVE simulations, I thought when i would try to reproduce results
with NAMD to validate an unfolding simulation protocol, all would be
easy. Nevertheless, I have not found yet an NVE simulation protocol
able to do that. Using
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 5
and timestep 2fs mantains energy very well (5 kcal/mol fluctuation in
500 ps) in a NVE dynamics in NAMD. I have test until 520K without
troubles, but the protein dont show any desire to be unfolded by
temperature before 0.5ns. This puzzling scenario make me ask which are
the differences beetween F3C and TIP3P. Maybe TIP3P with CHARMM is
unable to unfold proteins, the only simulation I done where unfolding
proceeds was in a SA from 500 to 600K at 1 atm, But the system
explodes.
Leonardo
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