Dear Callum,
The link that you provided (
https://fileexchange.imperial.ac.uk/files/2978c3d8102/DMPC_subbarao.tgz) is
not working. Can you send the exactly same files that you used (.prmtop and
.inpcrd) in the simulations of GAFFLipid paper.
Regards,
Subbarao kanchi
---------- Forwarded message ----------
From: Dickson, Callum <callum.dickson09.imperial.ac.uk>
Date: Wed, Oct 9, 2013 at 6:28 PM
Subject: FW: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
To: "ksubbuamber.gmail.com" <ksubbuamber.gmail.com>
Hi Subbarao,
Below is a link to a tarball containing the DMPC pdb, prmtop and
coordinates plus all the inputs I used for a bilayer run. Try repeating
this protocol on CPU and let me/Ross know what happens.
Regards,
Callum
------------------------------
*From:* Subbarao Kanchi [ksubbuamber.gmail.com]
*Sent:* 09 October 2013 09:44
*To:* Dickson, Callum
*Cc:* AMBER Mailing List; Ross Walker
*Subject:* Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
Dear Callum,
Thank you for your kind reply. I tested the GAFFLipid
force field extensively on CPUs. The area per lipid is going even less than
56 A^2 and bilayer getting freeze.I got 49 A^2 after 50 ns. I hope this
will be fixed in next coming amber force filed (Lipid 12).
thanking you all
Regards,
Subbarao Kanchi
On Wed, Oct 9, 2013 at 1:37 PM, Dickson, Callum <
callum.dickson09.imperial.ac.uk> wrote:
> Hi Subbarao,
>
> We have had a number of issues with bilayer simulations in amber related
> to the rapid collapse of the simulation box in the initial stages of
> simulation. These were a particular issue when using the GPU code. This
> affected the gafflipid work and mean the lipid parameters require more
> attention.
>
> As a consequence running a DMPC with gafflipid causes the area per lipid
> to drop to about 56A^2, which is below the experimental 60A^2 though the
> bilayer is still liquid phase.
>
> If you want to run DMPC at the experimental area per lipid using amber the
> following options are open to you:
>
> - use GAFF parameters by Lula Rosso with an applied surface tension
> (available on the Bryce website)
> - use GAFFlipid with a (lower) applied surface tension
> - wait for Lipid12 which will support DMPC and will be released soon
>
> Kind regards,
> Callum
>
> ------------------------------
> *From:* Subbarao Kanchi [ksubbuamber.gmail.com]
> *Sent:* 07 October 2013 06:05
> *To:* AMBER Mailing List
> *Cc:* Dickson, Callum; Ross Walker
> *Subject:* Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
>
> 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>
>>> >>>>
>>> >>>
>>> >>>
>>> >>
>>> >_______________________________________________
>>> >AMBER mailing list
>>> >AMBER.ambermd.org
>>> >http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Fri Oct 18 2013 - 07:30:06 PDT
