From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Jun 29 2011 - 17:49:51 CDT
Hi Ye,
I have never used the implicit solvent model of NAMD. Try changing the
parameters in the GBIS section of your input file. Does it unfold
immediately or after how many picoseconds? Also, what part exactly
unfolds, the entire protein or just the terminal repeats?
Gianluca
On Wed, 29 Jun 2011, Ye Yang wrote:
> Hi, Frencesco and Gianluca:
> Thanks for replying.
> Yes, it is the repeat Ankyrin protein... So maybe it is no good for using the
> implicit solvent?
> The problem right now is that I would like to pull the ankyrin protein at a certain
> temperature (300K), so I need to equilibrating it first, as long as it is stable in room
> temperature, it will be fine for me.
> For my case, some of my friends did coarse grained simulation in vacuum, yet they
> seem do not have any trouble in the unexpected unfolding, I am not sure what is going on if
> I use all-atom.
> Thank you very much.
> Ye
>
> 2011/6/29 Gianluca Interlandi <gianluca_at_u.washington.edu>
> I suspect that E3_19 might not be stable with this type of implicit solvent
> model (it doesn't contain a term to take the non-polar solvation energy into
> accout). You should simulate it in explicit water (or try one of the implicit
> solvent models implemented in CHARMM, but I doubt it).
>
> If by E3_19 you mean the designed Ankyrin Repeat Protein, I know people who
> tried different implicit solvent models a while ago. None really worked. But I
> might be mistaken and by no means I want to be discouraging.
>
> Gianluca
>
>
> On Wed, 29 Jun 2011, Francesco Oteri wrote:
>
> 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
>
>
>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>
>
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
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