Re: Re: Namd-I: Implicit solvent problem

From: Enrico Guarnera (enrico.guarnera_at_gmail.com)
Date: Wed Jul 20 2011 - 11:22:46 CDT

Hi there,

this happens because the GBIS model as implemented in NAMD 2.8 does not
include an implicit treatment of the hydrophobic effect or the non-polar
effects due to the solvent but only the electrostatics.
It would really great if the NAMD team could consider to address this
problem in a future version of the program (for example adding a SASA
module...).

Best,
Enrico

On Wed, Jul 20, 2011 at 12:04 PM, Matteo Rotter <matteo.rotter_at_uniud.it>wrote:

> Dear All,
>
> I have tried to perform simulation of this Ankyrin protein.
> I found some results that i would like to share with you. Please let me
> know what you think about.
>
> 1st: as Ye Yang wrote, the protein seems really stable in explicit solvent
> simulation.
> 2nd: in implicit solvent(gb): if i perform minimization and run in the same
> simulation (one .conf file) the protein rapidly unfolds in very few
> picoseconds.
> 3rd: in implicit solvent(gb): performing minimization and run with two
> different runs of namd will not affect the stability of protein. Also using
> same seed between 2nd and 3rd and inside 3rd between minimization and run.
>
> What do you think about?
>
> Regards,
> Matteo.
>
> Quoting Giovanni Settanni <gs_at_mrc-lmb.cam.ac.uk>:
>
> Maybe you may try the protocol that we used in this paper
>> http://www.ncbi.nlm.nih.gov/**pubmed/20371329>
>> to pull other similar ankyrin proteins. we used EE1 and FACTS implicit
>> solvent models that are available in charmm.
>>
>> On 06/30/2011 12:44 AM, Ye Yang wrote:
>>
>>> 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 <mailto:knightyangpku_at_gmail.*
>>> *com <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
>>> <mailto:gianluca_at_u.washington.**edu <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
>>> <mailto:gianluca_at_u.washington.**edu <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.
>>> ------------------------------**-----------------------
>>>
>>>
>>>
>>>
>>
>>
>
>
> ------------------------------**------------------------------**----------
> SEMEL (SErvizio di Messaging ELettronico) - CSIT -Universita' di Udine
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:13 CST