Re: [gmx-users] the FF parameter sets

2008-09-12 Thread Justin A. Lemkul
Chih-Ying Lin wrote: does it mean ? =>H - N - CH3 ( the angle between H - N - CH3, right?) H - N - H, H - N - (HC-6-ring) H - N - CHn (HC-6-ring) - NT -CHn CH3 - NT - CHn The angles you have listed are correct. -Justin thank you Lin

[gmx-users] the FF parameter sets

2008-09-12 Thread Chih-Ying Lin
Hi I read your comment. "This is a comment line to the previous one. The angle is between the three atoms mentioned. it is an index in another array in the gROMOS96 files (not part of gromacs) ." But, I did not understand.. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring

Re: [gmx-users] the FF parameter sets

2008-09-12 Thread David van der Spoel
Chih-Ying Lin wrote: Hi I have to ask the same question again. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 I confuse with the comma "," and " - " please read my previous answer. does it mean ? =>H - N - CH3 ( the angle between H - N - CH3, right?) H

[gmx-users] the FF parameter sets

2008-09-12 Thread Chih-Ying Lin
Hi I have to ask the same question again. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 I confuse with the comma "," and " - " does it mean ? =>H - N - CH3 ( the angle between H - N - CH3, right?) H - N - H, H - N - (HC-6-ring) H - N - CHn 90 (HC-6-r

Re: [gmx-users] the FF parameter sets

2008-09-11 Thread David van der Spoel
Chih-Ying Lin wrote: Hi I think that I did not described my question clearly. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 three atoms A, B, C form an angle. A-B-C what does this line mean? H - N - CH3. H, HC-6-ring, H-NT-CHn 90 This is a comment line to the pr

[gmx-users] the FF parameter sets

2008-09-11 Thread Chih-Ying Lin
Hi I think that I did not described my question clearly. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 three atoms A, B, C form an angle. A-B-C what does this line mean? H - N - CH3. H, HC-6-ring, H-NT-CHn 90 does it mean ? =>H - N - CH3 H - N - H, H - N

Re: [gmx-users] the FF parameter sets

2008-09-11 Thread Justin A. Lemkul
Chih-Ying Lin wrote: Hi I am looking into the FF parameter sets from the FF.itp. for example #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 I could not understand the last line. Please tell me what it means. ga_XX = Gromos Angle The sets of three atoms ind

[gmx-users] the FF parameter sets

2008-09-11 Thread Chih-Ying Lin
Hi I am looking into the FF parameter sets from the FF.itp. for example #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 I could not understand the last line. Please tell me what it means. Thank you Lin ___ gmx-users mail