Re: Namd-I: Implicit solvent problem

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Jun 29 2011 - 16:31:49 CDT

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.
-----------------------------------------------------

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:08 CST