[gmx-users] choice of forcefield

[Revthi Sanker]

Dear Sir,
Thank
 you so much for your reply. To be specific, my system has only four 
lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I 
was not able to get all atom parameters for these lipids from the lipid 
book( only united atom parameters were available). So I had resorted to 
using united atom for the whole system. But I am afraid if I am missing 
out on some crucial protein-drug interactions because of this united 
atom consideration.
Kindly guide me in this regard.
Thank you so much once again.

Yours sincerely,
Revathi
M.S.Research Scholar
Indian Institute of Technology Madras
India


--- On Tue, 28/5/13, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] choice of forcefield
To: gmx-users at gromacs.org
Date: Tuesday, 28 May, 2013, 1:30 PM

On 2013-05-28 14:39, massimo sandal wrote:
> What other people do?

Read literature. Gromacs allows you to choose many. If you need detailed 
results use an atomistic force field.
>
>
> 2013/5/28 Dr. Vitaly Chaban <vvchaban at gmail.com>
>
>> In my mind, MARTINI is a decent option to build your particular topology
>> upon.
>>
>> Dr. Vitaly Chaban
>>
>>
>> On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker <revthi.sanker at yahoo.com
>>> wrote:
>>
>>> Dear all,
>>> I am a beginner to performing simulations and my system consists of
>>> protein+ cholesteryl ester +phospholipid and drug. Papers involving
>> lipids
>>> are in general united atom, while those involving drug-protein systems
>> are
>>> all-atom mostly. Kindly suggest me which of these, all-atom or united
>> atom
>>> should I be using for my system.
>>>
>>> Thanks for your help in advance
>>> Yours sincerely,
>>> Revathi
>>> M.S. Research Scholar
>>> Indian Institute of Technology,Madras
>>> India
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
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