[gmx-users] any alternative methods?

[Albert]

hello Justin:

  thanks for reply.
  I've read both the paper and manual script. As indicated from the 
output, I found the following line:

368    4.295    3.8840018217

I just wondering how could it possible fro residue 368 with a value of 3.88?

For the pure lipids/water case, my apology for this since I forgot to 
change the box size values but the protein/lipids case is with correct 
box size.

best
Albert


On 08/22/2012 02:02 PM, Justin Lemkul wrote:
>
>
> On 8/22/12 3:16 AM, Albert wrote:
>> On 08/22/2012 08:23 AM, Mark Abraham wrote:
>>> 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
>>
>> Dear Mark:
>>
>>   thanks for kind comments. I also enlarge the grid size to 200 for 
>> my system.
>> And I get similar results. What need to mention is that I've got 
>> around 160 aa
>> are beruied in lipids and I don't know why only the following few 
>> were mentioned
>> in calculations.
>>
>
> I don't know what you mean by "only the following few."  The protein 
> is given one area value, as shown in the output file.  The remaining 
> lines correspond to lipid residues, with the resid corresponding to 
> each.  Embedded protein residues do not factor into the APL 
> calculation as they are not part of the grid surface used for the 
> calculation.  Please see our paper on GridMAT-MD and several of the 
> figures within that demonstrate how the algorithm is applied.
>
> I will also echo something Mark said - how does any of this relate to 
> the previous claim that GridMAT-MD does not reproduce the APL of a 
> pure bilayer? You've changed the topic here so it's hard to judge what 
> the question is at this point.  Your pure POPC membrane starts out 
> reasonably enough; if you stick a large protein into the membrane, the 
> structure likely changes and you're now comparing apples and oranges.  
> Your protein occupies about one-third of the total lateral area of 
> each leaflet, which may indicate that you do not have a membrane of 
> sufficient size to recover bulk lipid properties that one would expect 
> to see far away from the protein.
>
> -Justin
>
>> Ave APL = 50.4388701869839 sq. Ang
>>
>> protein    5.0    1580.671044407
>> Resid    Z-value    Area (sq. Ang.)
>> 354    3.675    64.6156666701
>> 355    3.725    50.2566296323
>> 356    2.97    34.4852282957
>> 357    4.028    52.4928731054
>> 358    3.217    58.2600273255
>> 359    3.821    22.362434731
>> 360    3.669    30.4835294491
>> 361    3.899    60.1431797239
>> 362    3.271    72.3836703135
>> 363    3.02    63.7917874958
>> 364    3.027    40.016988466
>> 365    3.406    67.087304193
>> 366    3.349    41.9001408644
>> 367    3.481    53.9052374042
>> 368    4.295    3.8840018217
>> 369    3.605    45.6664456612
>> 370    3.467    55.5529957528
>> 371    3.403    65.2041517946
>> 372    3.353    51.4335998813
>> 373    2.663    48.7265683086
>> 374    3.269    58.6131184002
>> 375    4.064    48.6088712837
>> 376    3.7    51.1982058315
>> 377    3.785    54.0229344291
>> 378    3.22    49.6681445078
>> 379    3.638    67.6757893175
>> 380    4.003    37.3099568933
>> 381    2.718    45.3133545865
>> 382    4.265    20.3615853077
>> 383    3.28    63.7917874958
>> 384    3.753    59.3193005496
>> 385    3.445    45.7841426861
>> 386    2.451    51.786690956
>> 387    4.336    44.4894754122
>> 388    3.554    67.5580922926
>> 389    2.911    40.2523825158
>> 390    3.447    78.857006683
>> 391    3.13    58.0246332757
>> 392    3.593    56.0237838524
>> 393    3.09    58.3777243504
>> 394    3.55    51.5512969062
>> 395    3.91    14.9475221623
>> 396    4.104    49.5504474829
>> 397    3.695    34.4852282957
>> 398    3.758    63.4386964211
>> 399    3.41    61.9086350974
>> 400    3.706    46.1372337608
>> 401    4.261    53.3167522797
>> 402    3.364    48.7265683086
>> 403    3.869    56.3768749271
>> 404    2.983    58.7308154251
>> 405    3.773    53.5521463295
>> 406    3.364    52.3751760805
>> 407    3.869    41.3116557399
>> 408    2.896    60.4962707986
>> 409    3.758    24.2455871294
>> 410    3.412    51.5512969062
>> 411    4.184    54.8468136034
>> 412    3.146    61.4378469978
>> 413    3.572    48.7265683086
>> 414    3.294    52.7282671552
>> 415    3.363    47.07880996
>