Dear Callum,
I hope that you do not see the mail. I hope it is good
to send you again for the reply.
Regards,
Subbarao Kanchi
On Sat, Oct 19, 2013 at 11:20 AM, Subbarao Kanchi <ksubbuamber.gmail.com>wrote:
> Dear Callum,
> Why don't you give the prmtop ans inpcrd files for same
> DMPC systems(72,288,512) that you provided in the link *
> http://lipidbook.bioch.ox.ac.uk/package/ *
> *
> *
> Now the DMPC that you provided is different (128DMPC+9KCL). This is
> different from the provided in link or reported in paper. The area per
> lipid that you mention is 56 A^2 also less than that of the reported in
> paper i.e 60.28 A^2. I am not able to understand that why is it different
> from the reported area per lipid. If I understand wrong, could you explain
> fully.
>
> Regards,
> Subbarao Kanchi
>
>
>
>
> On Fri, Oct 18, 2013 at 7:57 PM, Dickson, Callum <
> callum.dickson09.imperial.ac.uk> wrote:
>
>> Hi Subbarao,****
>>
>> ** **
>>
>> I think the link only stays active for one week. I have uploaded again so
>> please try this link now:
>> https://fileexchange.imperial.ac.uk/files/4952c6b992c/DMPC_subbarao.tgz**
>> **
>>
>> ** **
>>
>> Best,****
>>
>> Callum****
>>
>> ** **
>>
>> *From:* Subbarao Kanchi [mailto:ksubbuamber.gmail.com]
>> *Sent:* 18 October 2013 15:22
>> *To:* Dickson, Callum; Ross Walker; AMBER Mailing List
>> *Subject:* Fwd: FW: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at
>> 303 K.****
>>
>> ** **
>>
>> 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****
>>
>> ** **
>>
>> ** **
>>
>> ** **
>>
>> ** **
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 27 2013 - 18:00:02 PDT
