[gmx-users] any alternative methods?

[Albert]

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.

best
Albert




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