From: Ye Yang (knightyangpku_at_gmail.com)
Date: Wed Jun 29 2011 - 17:44:55 CDT
Also, if I use explicit solvent, this protein will be very stable at 400K
for 10 ns simulation, which is not experimentally true, and I need a box of
~60nm waterbox. Any suggestions which approach should I use?
Thanks
Ye
2011/6/29 Ye Yang <knightyangpku_at_gmail.com>
> 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.
>> ------------------------------**-----------------------
>>
>
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:30 CST