From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Feb 24 2014 - 10:29:42 CST
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
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