Re: Namd-I: Implicit solvent problem

From: Francesco Oteri (francesco.oteri_at_gmail.com)
Date: Wed Jun 29 2011 - 16:17:21 CDT

Hi Ye,
maybe you are using a too small cut-off..Try with a value greater than 30A

Francesco

Il 29/06/2011 23:07, Ye Yang ha scritto:
> 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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