From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Mon Jul 28 2014 - 12:08:15 CDT
I missed to indicate the simulation time in the previous mail. We simulated
upto 60ns.
On Mon, Jul 28, 2014 at 7:06 PM, Bala subramanian <bala.biophysics_at_gmail.com
> wrote:
> Hi,
> We have used charmm 2b7 ff for the assembly, we simulated it in NVT
> ensemble with electric field applied to see ionic passage.
>
> The experimental evidence suggest a pore opening of up to 10A while we
> have ~2 Ang opening. The observations are based on pore dimension
> estimations.
>
>
>
>
> On Mon, Jul 28, 2014 at 5:57 PM, Kenno Vanommeslaeghe <
> kvanomme_at_rx.umaryland.edu> wrote:
>
>> What force field are you using? How long did you simulate? How did you
>> quantify "conformational changes"? How different is it from "experiment"?
>>
>> On 07/28/2014 11:19 AM, Bala subramanian wrote:
>>
>>> Friends,
>>>
>>> I am new to membrane protein simulations. We have simulated a protein in
>>> a
>>> DOPC bilayer at 303K and we found that the level of protein
>>> conformational
>>> changes is not similar to what has been observed in experiments. My PI
>>> suggested to try higher temperature like 320K to see if we are able to
>>> see
>>> larger changes in the conformation.
>>>
>>> I am looking fwd to hear from any of you with experience in memb-prot
>>> simulation if such high temperature can be attempted with DOPC bilayer.
>>> Any information on some relevant literature would be of great help.
>>>
>>> Thank You,
>>> Bala
>>>
>>> --
>>> C. Balasubramanian
>>>
>>
>>
>
>
> --
> C. Balasubramanian
>
-- C. Balasubramanian
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