*Dear callum and Balazs*,
*I have performed the DMPC simulation
(for 288 lipid patch) with this GAFFLipid parameter (provided at the lipid
book
http://lipidbook.bioch.ox.ac.uk/package/). I got the area per Lipid
~55.22 sq Angstroms/lipid after 10ns but it is far away from the reported
value in the paper "GAFFlipid: a General Amber Force Field for the accurate
molecular dynamics simulation of phospholipid" (60.38 sq Angsroms/lipid). I
would appreciate any suggestion in this regards. *
*
*
*Regards,*
*Subbarao kanchi. *
On Wed, Sep 25, 2013 at 1:00 AM, Subbarao Kanchi <ksubbuamber.gmail.com>wrote:
> Hi Balazs,
> Thank you for the reply and I am trying the new parameters
> form this Lipidbook link.I will update the results of this new parameters.
>
>
> Regards,
> Subbarao Kanchi
>
>
> On Tue, Sep 24, 2013 at 11:32 PM, <jojartb.jgypk.u-szeged.hu> wrote:
>
>> Dear Subbaro,
>> The parameters of that website is not GAFFLipid.
>> Download the correct parameters and coordinate files from
>> http://lipidbook.bioch.ox.ac.**uk/ <http://lipidbook.bioch.ox.ac.uk/>.
>> Hope this helps.
>> Best regards, Balazs
>>
>> Idézet (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<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<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<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<http://lists.ambermd.org/mailman/listinfo/amber>*
>>>>>
>>>>>
>>>>>
>>>> ______________________________**_________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.org/mailman/listinfo/amber>
>>>
>>
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 27 2013 - 11:30:02 PDT
