Hi Callum and Ross,
Than you for your reply. I did not use any
amber GPU version. I used only the amber 10 CPU version.As you both
suggested, I corrected the hydrogen mass from 1.088 to 1.088 in
GAFFlipid.frcmod file and rerun the simulation still the DMPC bilayer is
freezing at 303K. It will be great if you provide correct parameters and I
would appreciate receiving any suggestion in this regard.
With regards,
Subbarao Kanchi.
On Wed, Aug 21, 2013 at 7:25 PM, Subbarao Kanchi <ksubbuamber.gmail.com>wrote:
> Dear Amber users,
> I am trying to reproduce the* DMPC* lipid membrane
> simulation using* GaffLipid* force field at the temperature *303* K as
> reported in the paper (*GAFFlipid: a General Amber Force Field for the
> accurate molecular dynamics simulation of phospholipid* ). I used the
> equilibrated DMPC membrane (*288dmpc_100ns.pdb,* *
> DMP.lib,GAFFlipid.frcmod, GAFFlipid.dat*) provided at
> http://www.pharmacy.manchester.ac.uk/bryce/amber. The membrane should be
> in melted phase (L_alpha phase) as reported in the paper but I am getting
> the Gel phase at same temperature (303K) with in 10 ns simulation. The
> reported area per lipid of DMPC at 303 K is ~61 square angstroms per lipid
> but I am getting the area per lipid ~50 square angstroms per lipid and
> membrane comes in gel phase. I would appreciate receiving any suggestion in
> this regard.
>
>
>
> Regards,
> Subbarao Kanchi.
>
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Received on Sat Sep 21 2013 - 00:30:03 PDT
