From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 24 2014 - 10:49:58 CST
On Mon, Feb 24, 2014 at 11:48 AM, Roy Fernando <roy.nandos_at_gmail.com> wrote:
> Hi Aron,
>
> Yes. They are nicely flexible (wiggly) but do not diffuse through the cell.
you are aware, that PEG-Water in high concentration forms all kinds of
self-assemblies, right?
axel.
>
> Thanks,
>
>
>
> On Mon, Feb 24, 2014 at 11:29 AM, Aron Broom <broomsday_at_gmail.com> wrote:
>>
>> what do you mean by the thermal movement? You mean they are just rigid
>> for 4ns? Or do you mean they are nicely flexible and at the right
>> temperature, but they don't diffuse through the cell?
>>
>>
>> On Mon, Feb 24, 2014 at 11:22 AM, Roy Fernando <roy.nandos_at_gmail.com>
>> wrote:
>>>
>>> Hi Kenno and NAMD Community
>>>
>>> I ran a PEG in water simulation using these force field parameters. The
>>> system contains a high percentage (40%) of PEG 400. After minimization and
>>> very slow heating I equilibrated this system for about 4ns (so far). I am
>>> observing PEG molecules undergoing all possible conformational changes as I
>>> would have expected for a small polymer in a solution. However I do not get
>>> to see thermal movement of the PEG molecules as a whole.
>>>
>>> I wonder if someone has any advise regarding what is going on in the
>>> simulation.
>>>
>>> Thanks in advance.
>>>
>>> Roy
>>>
>>>
>>>
>>>
>>> On Wed, Nov 6, 2013 at 2:58 PM, Roy Fernando <roy.nandos_at_gmail.com>
>>> wrote:
>>>>
>>>> Hi Kenno,
>>>>
>>>> Yes it is top_all35_ethers.rtf and par_all35_ethers.prm. Thanks for
>>>> clarification.
>>>>
>>>> I noticed there is existing work using these parameters for PEGylated
>>>> lipids and micelles. However, I did not find existing work for simulating
>>>> PEG with protein. Your response was helpful to carry out the work with some
>>>> confidence. I will look into verification of the results with experimental
>>>> data.
>>>>
>>>> Regards,
>>>>
>>>> Roy
>>>>
>>>>
>>>>
>>>>
>>>> On Wed, Nov 6, 2013 at 2:27 PM, Kenno Vanommeslaeghe
>>>> <kvanomme_at_rx.umaryland.edu> wrote:
>>>>>
>>>>> - I know of no top_all35_ethers-oh.rtx file; to be safe, it's probably
>>>>> best to use top_all35_ethers.rtf and par_all35_ethers.prm from the official
>>>>> force field distribution.
>>>>>
>>>>> - There is a large body of evidence suggesting that the (mostly
>>>>> water-oriented) CHARMM parameter optimization procedure yields relatively
>>>>> well-balanced interactions between different CHARMM solutes (eg. protein and
>>>>> a PEG chain) in TIP3P water (except for ions, which sometimes require NBFIX
>>>>> terms). Therefore, I would expect the PEG parameters to be appropriate for
>>>>> your purpose. It never hurts to verify against experimental data that is
>>>>> directly relevant to your project, though.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 11/06/2013 01:21 PM, Roy Fernando wrote:
>>>>>>
>>>>>> Hello NAMD experts
>>>>>>
>>>>>> I plan to run a protein simulation with Polyethylene Glycol (PEG).
>>>>>>
>>>>>> I notice that there exist CHARMM force filed parameters for PEG
>>>>>> (top_all35_ethers-oh.rtx). from previous work (Vorobyov et al. 2007
>>>>>> and
>>>>>> Lee et al 2008). However, those parameter are developed for PEG
>>>>>> interaction with water.
>>>>>>
>>>>>> I wonder if these parameters are still good for equilibrating protein
>>>>>> with
>>>>>> PEG?
>>>>>>
>>>>>> Thanks a lot , in advance.
>>>>>>
>>>>>> Roy
>>>>>
>>>>>
>>>>
>>>
>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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