[gmx-users] Re: Simulating a semi-membrane protein

[pavithrakb]

Thank you both of you for taking time to help me..
This would be definitely useful. 
thank you so much. 



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Re: [gmx-users] Re: Simulating a semi-membrane protein

[Catarina Santos]

Dear Pavithrakb,

First of all, your choice will depend on the available parameters for the
lipid molecules that you want to simulate (check the Lipidbook
repository
).

Concerning the GROMOS force fields the most recent lipid parameters are the
ones included in the G54A8 force field (Reif_2012_JCTC_8_3705,
Reif_2013_JCTC_9_1247).

However, Poger et al proposed an add-on to the standard G53A6
(Poger_2010_JCC_31_1117
and Poger_2010_JCTC_6_325), lately incorporated in the G54A7
(Schmidt_2011_EBJ_40_843), that is commonly used and yields good results
for the analysed lipid parameters (i.e. in agreement with experimental
measurements).

Despite the aforementioned papers, you might want to go through the
references listed bellow concerning several lipid parameters for GROMOS
force fields or proposed modifications (e.g. cutoff schemes, charges,
charge group distributions):

- Berger lipids: Berger_1997_JB_72_2010
- Ash lipids: Tieleman_2006_JPCM_18_S1221
- G43A1-S3: Chiu_2009_JPCB_113_2748
- G45A3: Schuler_2001_JCC_22_1205, Chandrasekhar_2003_EBJ_32_67
- Modified Berger: Anezo_2003_JPCB_107_9424
- Modified ffG45A3: Anezo_2003_JPCB_107_9424
- Kukol lipids: Kukol_2009_JCTC_5_615
- G53A6L: Poger_2010_JCC_31_1117, Poger_2010_JCTC_6_325
- G54A7: Schmidt_2011_EBJ_40_843
- G54A8: Reif_2012_JCTC_8_3705, Reif_2013_JCTC_9_1247

-- 

Catarina Santos
Research Student
Molecular Simulation Group
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Av.da República, Apartado 127
2781-901 Oeiras, Portugal
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Re: [gmx-users] Re: Simulating a semi-membrane protein

[Justin Lemkul]

On 7/23/13 7:46 AM, pavithrakb wrote:

Sir,
I'm new to simulation. is there any papers or materials (book or website) to
learn about the forcefields and their limitations. All the advice I get from
people is to select a ff and membrane based on the previous works on that
protein or protein family. I know its too much to ask but, can you please
suggest some papers/materials on forcefields and selecting a membrane. I'm
sure it will be useful to many beginners like me.


You already have a good starting point - identify what others do.  Precedent is 
important.  Then ask yourself, why are others doing what they are doing?  To 
answer that question requires quite a bit of reading.  Several days spent 
reading about different force fields will save you months of wasted time if you 
blindly choose a poor one for your simulations.  The primary literature for many 
force fields goes back over the course of decades, which will give you an 
appreciation for the underlying design, assumptions, and implementation of a 
force field.  More recent articles certainly exist that have challenged these 
force fields under different conditions.


Websites and textbooks would be convenient, but I have never seen anything 
comprehensive on this topic.  Maybe someone else has and can suggest it.  There 
is, however, a vast amount of literature that tests different force fields. 
Some names that come to mind include Bert de Groot and Robert Best, who I know 
have published several very nice force field comparisons, in addition to the 
publications of the labs from which the force fields originate.  Expect to 
occupy a lot of time reading before doing any simulations - it is time well spent.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: Simulating a semi-membrane protein

[pavithrakb]

Sir,
I'm new to simulation. is there any papers or materials (book or website) to
learn about the forcefields and their limitations. All the advice I get from
people is to select a ff and membrane based on the previous works on that
protein or protein family. I know its too much to ask but, can you please
suggest some papers/materials on forcefields and selecting a membrane. I'm
sure it will be useful to many beginners like me. 
Thankyou. 



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Re: [gmx-users] Re: Simulating a semi-membrane protein

[Justin Lemkul]

On 7/22/13 10:21 PM, pavithrakb wrote:

Dear Sir,
Thank you.
I understand it now. But, when apply the force field, should I select the
membrane ff like gromos56 (like in your KALP tutorial) or will it be a
complex process to select a ff?



Choosing a force field is always complicated.  There are numerous factors to 
consider and one must be knowledgeable about the different force fields, their 
applications to similar systems, and known defects or limitations.  Choosing the 
same force field just because it is used as an example in a tutorial is a poor 
reason.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: Simulating a semi-membrane protein

[pavithrakb]

Dear Sir,
Thank you.
I understand it now. But, when apply the force field, should I select the
membrane ff like gromos56 (like in your KALP tutorial) or will it be a
complex process to select a ff? 



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[gmx-users] Re: Simulating a semi-membrane protein

[pavithrakb]

Dear Sir,
Thank you.
I understand it now. But, when apply the force field, should I select the
membrane ff like gromos56 (like in your KALP tutorial) or will it be a
complex process to select a ff?




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