From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Mon Feb 24 2014 - 10:48:08 CST
Hi Aron,
Yes. They are nicely flexible (wiggly) but do not diffuse through the cell.
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
>
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