[gmx-users] any alternative methods?

[Mark Abraham]

On 22/08/2012 3:47 PM, Albert wrote:
> On 08/22/2012 07:44 AM, Mark Abraham wrote:
>>
>> I don't see how this relates to your claim that you computed a value 
>> with GridMAT that doesn't relate to a value computed some other way.
>>
>> Mark 
>
> HI Mark:
>
>  thanks for kind reply.
>
>
> here is my parameter for for calculation. The vector values was take 
> from the bottom of .gro file.
>
>
> ###### Input file and input file parameters
>
> bilayer            npt.gro
> solvent            SOL
> ions            NA+,CL-
>
> resname        POPC
> atomname        P1,C1
>
> ###### Define the size and shape of the grid
>
> box_size        solvent
> vectors            6.84452,6.84452,9.80113
> grid            20

The authors use a 200x200 grid in their first published work with this 
tool. What makes you think 20 is enough? (And even if it is enough, you 
still haven't demonstrated another calculation showing that the APL with 
the embedded protein should be different.)

Mark

> conserve_ratio yes
>
> ###### Define whether there is a protein embedded in the bilayer
>
> protein            yes
> precision        1.3
> P_value            5.0
>
> ###### Define the desired output files
>
> #top_pbc            yes
> #bottom_pbc        yes
> #average_pbc        yes
>
> top_area        yes
> bottom_area        yes