[gmx-users] question

[Thomas Piggot]

I guess the force field to use is a bit down to choice, however I would 
say that there are several force fields which should not be used in this 
case. There are several force fields/parameterisations that do not 
behave well for these two types of lipids (e.g. many Berger based 
parameters). As suggested, a thorough search through the literature is 
really what you need to do (e.g. for PG 
http://pubs.acs.org/doi/abs/10.1021/jp900645z ; for both (and apologies 
for the self promotion) the supp info from 
http://pubs.acs.org/doi/abs/10.1021/jp207013v and many more papers that 
are out there). For making a choice between force fields you should 
weigh up things like accuracy, speed of simulation, lipid diffusion 
rates, inclusion of other components of your system (e.g. proteins, 
etc.) and so on.

Cheers

Tom

On 02/03/2014 07:06 PM, Justin Lemkul wrote:
>
>
> On 2/3/14, 2:03 PM, nafas wrote:
>> Hi
>> thanks for your help.
>> I think charmm force field imust use.but i dont know who can i found  
>> its files ?
>>
>
> The full CHARMM36 force field in Gromacs format can be obtained from 
> http://mackerell.umaryland.edu/CHARMM_ff_params.html.
>
> -Justin
>
>>
>> On Monday, February 3, 2014 9:19 PM, Justin Lemkul <jalemkul at vt.edu> 
>> wrote:
>>
>>
>> On 2/3/14, 12:30 PM, nafas wrote:
>>  > Hi
>>  > I am tring with mixture pope/popg for simulatie membrane bacteria 
>> that i use
>> of gromos53a6 force field.
>>  > what force field should i use?charmm force field?
>>  >
>>
>> What does your scrutiny of the literature tell you?  Which force 
>> field succeeds
>> in the most meaningful ways?
>>
>>
>>  > in program  have been used pope.itp ,popg.itp, .....files .
>>  > I want to run grompp command but give afatall error:not found NH3L 
>> atomtype.
>>  > grompp -f minim.mdp -c ......gro -p ....top -o em.tpr
>>  >
>>  > I dont know what is problem?
>>
>>
>> You have not constructed the force field correctly.  Without 
>> significantly more
>> detail, there's nothing useful to suggest beyond a thorough read 
>> through Chapter
>> 5 of the manual.
>>
>> -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
>>
>> jalemkul at outerbanks.umaryland.edu 
>> <mailto:jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>>
>> ==================================================
>>
>>
>

-- 
Dr Thomas Piggot
University of Southampton, UK.