From: Ye Yang (knightyangpku_at_gmail.com)
Date: Wed Jun 29 2011 - 16:07:55 CDT
Dear Namd expert:
I am trying to use implicit solvent model to simulate my protein E3_19,
which is thermally stable through experiment and full molecule
simulation(above 400K in simulation for over 10ns).
However, once I am using the imlicit solvent, it even unfolds at 300K,
which is really weird, could anyone explain to me what is happening and how
I can solve this?
Also, what I am thinking is to increase the damping factor, but what
should I typically use?
Thank you very much.
exclude scaled1-4
1-4scaling 1.0
cutoff 18.
switching on
switchdist 12.
pairlistdist 22
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temp
langevinHydrogen no ;# don't couple langevin bath to hydrogens
if {1} {
GBIS on
solventDielectric 78.5
intrinsicRadiusOffset 0.09
ionConcentration 0.2
GBISDelta 1.0
GBISGamma 4.85
alphaCutoff 15
}
No BC and No PME for my simulation
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