From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Mon Feb 24 2014 - 10:22:47 CST
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
Thanks in advance.
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
> 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
> 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
>>> Thanks a lot , in advance.
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