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

From: <jojartb.jgypk.u-szeged.hu>
Date: Tue, 24 Sep 2013 20:02:48 +0200

Dear Subbaro,
The parameters of that website is not GAFFLipid.
Download the correct parameters and coordinate files from
http://lipidbook.bioch.ox.ac.uk/.
Hope this helps.
Best regards, Balazs

Id├ęzet (Subbarao Kanchi <ksubbuamber.gmail.com>):

> Hi Ross,
>
> Strong apologies for multiple time post. It was happen because there is
> problem to my amber mailing-list account setting and I was not sure that
> the mail was posted.
>
> I simply changed the mass number and I do not get the new VDW parameters.
> Callum mentioned that the rest of uploaded parameters are correct. I am
> fallowing the same protocol and input parameters (same thermostat and
> pressure couplings etc) that are mentioned in the force field paper (
> GAFFlipid: a General Amber Force Field for the accurate molecular dynamics
> simulation of phospholipid ) and the parameters that I downloaded are from
> this link http://www.pharmacy.manchester.ac.uk/bryce/amber.
>
> With regards,
> Subbarao Kanchi.
>
>
>
>
> On Tue, Sep 24, 2013 at 10:05 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> 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]
>>> 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 - 11:30:03 PDT
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