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>*
>>>>
>>>>
>>>>
>>> ______________________________**_________________
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>>
>
>
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Received on Tue Sep 24 2013 - 13:00:02 PDT
