Namd-I: Implicit solvent problem

From: Ye Yang (
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} {
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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