Dear Ross,
I would like to know problem in using the DMPC GAFFLipid
force field.I already attached my Amber input file and I would appreciate
any suggestion from you.
Regards,
Subbarao Kanchi
On Wed, Oct 2, 2013 at 7:55 AM, Subbarao Kanchi <ksubbuamber.gmail.com>wrote:
>
> Dear Ross,
> I follow the following protocol.
> 1) minimization 10000 (steepest descant) + 5000 (conjugate gradient)
> 2) Heating (from 0 to 303 K)
> 3) production run (amber input file is attached *md.in*)
>
> Making DMPC bilayer system.
> I have used the same bilayer patch that provided in the Lipid book
> (288_dmpc.pdb), library (DMP.lib) and parameter file (GAFFLipid.frcmod).
>
> the input files are prepared in Xleap
>
>
> source leaprc.ff10
> source leaprc.gaff
> source GAFFlipid.dat
> loadamberparams GAFFlipid.frcmod
> loadoff DMP.lib
> lipid = loadpdb 288dmpc_100ns.pdb
> setBox lipid centers
> saveamberparm lipid 288dmpc.prmtop 288dmpc.inpcrd
>
>
> the .prmtop and .inpcrd files were used for the amber simulations.
> The amber version is
> -------------------------------------------------------
> Amber 10 SANDER 2008
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 10
>
>
>
>
>
>
>
> On Tue, Oct 1, 2013 at 9:34 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Subbarao,
>>
>> I believe Callum is on vacation right now so it might be a while before
>> someone has the time to try things out here and find out why you are
>> seeing problems. In the meantime it would be helpful if you could post
>> your entire simulation procedure from structure generation all the way to
>> you seeing it freezing. Also please let us know the specific version of
>> AMBER you are using, command lines and the patch level of the code. Lipid
>> simulations are extremely sensitive to the way the MD is carried out so it
>> is critical to know this information in order to figure out why you are
>> seeing problems.
>>
>> All the best
>> Ross
>>
>>
>> On 9/30/13 11:14 AM, "Subbarao Kanchi" <ksubbuamber.gmail.com> wrote:
>>
>> >*Dear Amber users,*
>> >* I have used the GAFF Lipid parameters
>> >(**provided
>> >at the lipid book http://lipidbook.bioch.ox.ac.uk/package/)** for DMPC
>> >and
>> >not able to get the reported area per lipid (was run number of times).
>> May
>> >I ask Authors of GAFFLipid paper (GAFFlipid: a General Amber Force Field
>> >for the accurate molecular dynamics simulation of phospholipid) for the
>> >correct
>> >GAFFLipid parameters. *
>> >*
>> >*
>> >*
>> >*
>> >*
>> >*
>> >*Regards,*
>> >*Subbarao Kanchi. *
>> >
>> >
>> >---------- Forwarded message ----------
>> >From: Subbarao Kanchi <ksubbuamber.gmail.com>
>> >Date: Fri, Sep 27, 2013 at 11:52 PM
>> >Subject: Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K.
>> >To: jojartb.jgypk.u-szeged.hu
>> >Cc: AMBER Mailing List <amber.ambermd.org>, Ross Walker <
>> >ross.rosswalker.co.uk>, callum.dickson09.imperial.ac.uk
>> >
>> >
>> >*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.pharmac
>> >>>>>>y.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.ambe
>> >>>>>>rmd.org/mailman/listinfo/amber>*
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>> ______________________________**_________________
>> >>>> AMBER mailing list
>> >>>> AMBER.ambermd.org
>> >>>>
>> >>>>http://lists.ambermd.org/**mailman/listinfo/amber<
>> http://lists.ambermd.
>> >>>>org/mailman/listinfo/amber>
>> >>>>
>> >>>
>> >>>
>> >>
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Received on Sun Oct 06 2013 - 22:30:03 PDT
