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

From: Subbarao Kanchi <ksubbuamber.gmail.com>
Date: Wed, 2 Oct 2013 07:55:11 +0530

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>*
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> ______________________________**_________________
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> >>>> AMBER.ambermd.org
> >>>>
> >>>>http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd
> .
> >>>>org/mailman/listinfo/amber>
> >>>>
> >>>
> >>>
> >>
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Received on Tue Oct 01 2013 - 19:30:04 PDT
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