Hi Subbarao,
I am not entire sure why you posted this question multiple times to the
mailing list. Often it can take several days before people find the time to
reply.
I would start by asking whether you simply just changed the H mass or you
actually went and got the new VDW parameters as well. What was the exact
procedure you used - with out knowing this it is difficult to know
specifically parameters you used.
All the best
Ross
From: Subbarao Kanchi <ksubbuamber.gmail.com>
Date: Tuesday, September 24, 2013 1:56 AM
To: <callum.dickson09.imperial.ac.uk>, Ross Walker <ross.rosswalker.co.uk>
Cc: <amber.ambermd.org>
Subject: Re: DMPC GAFF lipid membrane is freezing at 303 K.
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 <http://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
> <http://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://AMBER.ambermd.org>
>> >http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 24 2013 - 10:00:03 PDT
