From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Mon Jul 28 2014 - 12:06:34 CDT
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 <
> 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:
>> 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,
>> C. Balasubramanian
-- C. Balasubramanian
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