From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Jul 28 2014 - 12:40:18 CDT
(1) There is no CHARMM 2b7. The previous _CGenFF_ release was 2b7, but
CGenFF cannot/should not be used for biomolecules. As for the biomolecular
force field, there is:
* the CHARMM22 protein parameter set (~1992).
* the CHARMM27 lipid parameter set (~2000).
* the CHARMM22/CMAP protein parameter set (~2003), which was often used
together with CHARMM27. Although obsolete, this combination still appears
to be popular with VMD and NAMD users.
* the CHARMM36 force field (~2012), which covers all classes of molecules
(including proteins and lipids) and has a number of important improvements
that may be relevant to your problem.
(2) Just checking; does experiment indicate it takes only 60ns at room
temperature for the pore to open up to 10A ?
On 07/28/2014 01:08 PM, Bala subramanian wrote:
> 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 <mailto: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 <mailto: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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