Hi Callum and Ross,
> Thank 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.
>
>
>
>
> Hi Subbarao,
>
> So the hl mass should be 1.008. The parameters on Lipidbook have been updated
> and I will see that the Bryce website is also updated.
>
> As Ross mentioned there previously was a bug in the GPU code that gave us
> issues with bilayer simulations, including the gafflipid work. Just now we
> are working to update the Lipid11 parameters, this will include support for
> DMPC bilayers.
>
> Callum
> ________________________________________
> From: Ross Walker [ross.rosswalker.co.uk]
> Sent: 21 August 2013 18:42
> To: AMBER Mailing List
> Cc: Dickson, Callum
> Subject: Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K.
>
> Hi Subbarao,
>
> A couple of things.
>
> 1) Can you confirm which version of AMBER you are using to run these
> simulations and if it is fully patched. In particular if you are using the
> GPU version make sure it is patched to at least v12.3 (bug fix.18) since
> there were a number of bugs discovered related to pressure control in
> lipid simulations - especially in cases where the initial box size
> changes
> considerably. This bug appeared if the box shrunk too much and if it did
> would create a feedback loop leading to the box shrinking further giving
> you a gel phase.
>
> 2) I just checked the parameters from the website you list and they
> appear
> to have not been properly updated.
>
> Specifically the frcmod file appears to still have the incorrect H mass
> (and thus H vow params) included:
>
> g3 12.010 0.878 same as c3
> hl 1.088 0.135 same as hc
>
>
> I am cc'ing Callum here who can verify for you what the new parameters
> should be and where to download them from. Callum can you also make sure
> the manchester website is updated please.
>
> All the best
> Ross
>
>
>
> On 8/21/13 6:55 AM, "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. *
> *>_______________________________________________ *
> *>AMBER mailing list *
> *>AMBER.ambermd.org *
> *>http://lists.ambermd.org/mailman/listinfo/amber *
>
>
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Received on Tue Sep 24 2013 - 02:00:05 PDT
