[AMBER] DMPC GAFF lipid membrane is freezing at 303 K.

From: Subbarao Kanchi <ksubbuamber.gmail.com>
Date: Sun, 22 Sep 2013 15:18:28 +0530

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.

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

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 Sun Sep 22 2013 - 03:00:02 PDT
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