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 - 10:30:03 PDT
