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<mailto: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<
http://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<mailto: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<mailto: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<mailto: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<mailto:jojartb.jgypk.u-szeged.hu>
>Cc: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>, Ross Walker <
>ross.rosswalker.co.uk<mailto:ross.rosswalker.co.uk>>, callum.dickson09.imperial.ac.uk<mailto: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<mailto: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<mailto: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<mailto: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://manchester.ac.uk/bryce/amber><http://www.pharmacy.
>>>>manchester.ac.uk/bryce/amber<http://manchester.ac.uk/bryce/amber>>
>>>> .
>>>>
>>>> With regards,
>>>> Subbarao Kanchi.
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Sep 24, 2013 at 10:05 PM, Ross Walker <ross.rosswalker.co.uk<mailto: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<mailto:ksubbuamber.gmail.com>>
>>>>> Date: Tuesday, September 24, 2013 1:56 AM
>>>>> To:
>>>>><callum.dickson09.imperial.ac.**uk<callum.dickson09.imperial.ac.uk<mailto:callum.dickson09.imperial.ac.uk>>>,
>>>>> Ross Walker <ross.rosswalker.co.uk<mailto:ross.rosswalker.co.uk>>
>>>>> Cc: <amber.ambermd.org<mailto: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<http://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<http://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://manchester.ac.uk/bryce/amber><http://www.pharmac
>>>>>>y.manchester.ac.uk/bryce/amber<http://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://AMBER.ambermd.org> *
>>>>>>
>>>>>>*>http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambe
>>>>>>rmd.org/mailman/listinfo/amber<http://rmd.org/mailman/listinfo/amber>>*
>>>>>>
>>>>>>
>>>>>>
>>>>> ______________________________**_________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>>>>
>>>>http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.
>>>>org/mailman/listinfo/amber>
>>>>
>>>
>>>
>>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto: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 Wed Oct 09 2013 - 01:30:04 PDT
