Re: [gmx-users] any alternative methods?

2012-08-22 Thread Albert
On 08/22/2012 03:58 PM, Justin Lemkul wrote: On 8/22/12 9:54 AM, Albert wrote: hello Justin: thanks for reply. I've checked this residue, it is close to protein but I am still curious for the value with 3.88. Even we also observe something 11, 13 which are the same weired to me. here

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Justin Lemkul
On 8/22/12 9:54 AM, Albert wrote: hello Justin: thanks for reply. I've checked this residue, it is close to protein but I am still curious for the value with 3.88. Even we also observe something 11, 13 which are the same weired to me. here is the screen shot for this residue. https://dl.

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Albert
hello Justin: thanks for reply. I've checked this residue, it is close to protein but I am still curious for the value with 3.88. Even we also observe something 11, 13 which are the same weired to me. here is the screen shot for this residue. https://dl.dropbox.com/u/56271062/1.jpg thanks

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Justin Lemkul
On 8/22/12 9:12 AM, Albert wrote: hello Justin: thanks for reply. I've read both the paper and manual script. As indicated from the output, I found the following line: 3684.2953.8840018217 I just wondering how could it possible fro residue 368 with a value of 3.88? My guess wo

Re: [gmx-users] any alternative methods?

2012-08-22 Thread 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: 3684.2953.8840018217 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 thi

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Justin Lemkul
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

Re: [gmx-users] any alternative methods?

2012-08-22 Thread 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 diff

Re: [gmx-users] any alternative methods?

2012-08-21 Thread 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

Re: [gmx-users] any alternative methods?

2012-08-21 Thread Albert
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 And here is the results. As we can see The values is really low. However, when I visulizaed the system i

Re: [gmx-users] any alternative methods?

2012-08-21 Thread Albert
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 tak

Re: [gmx-users] any alternative methods?

2012-08-21 Thread Mark Abraham
On 22/08/2012 3:34 PM, Albert wrote: On 08/21/2012 08:25 AM, Mark Abraham wrote: Since that calculation is one of the main purposes of GridMAT, I'd suspect you're comparing two different quantities, or not calculating one correctly. Mark -- I am very curious about this. The initial ALP for

Re: [gmx-users] any alternative methods?

2012-08-21 Thread Albert
On 08/21/2012 08:25 AM, Mark Abraham wrote: Since that calculation is one of the main purposes of GridMAT, I'd suspect you're comparing two different quantities, or not calculating one correctly. Mark -- I am very curious about this. The initial ALP for my equilibrated POPC system is someth

Re: [gmx-users] any alternative methods?

2012-08-21 Thread Justin Lemkul
On 8/21/12 2:25 AM, Mark Abraham wrote: On 21/08/2012 4:00 PM, Albert wrote: Dear: I am going to calculate the area/lipids for my membane system and I found that GridMAT for area/lipids calculation is not that reliable since I calculate by XY/(0.5 lipids number) for the pure well equilbirat

Re: [gmx-users] any alternative methods?

2012-08-20 Thread Mark Abraham
On 21/08/2012 4:00 PM, Albert wrote: Dear: I am going to calculate the area/lipids for my membane system and I found that GridMAT for area/lipids calculation is not that reliable since I calculate by XY/(0.5 lipids number) for the pure well equilbirated POPC lipids system, my values is 67 w

[gmx-users] any alternative methods?

2012-08-20 Thread Albert
Dear: I am going to calculate the area/lipids for my membane system and I found that GridMAT for area/lipids calculation is not that reliable since I calculate by XY/(0.5 lipids number) for the pure well equilbirated POPC lipids system, my values is 67 which is close to experimental data bu