Re: [gmx-users] About Solvation of Lipid Protein

2012-10-27 Thread Justin Lemkul
On 10/27/12 5:16 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply I am following your Protein-lipid Tutorial ( KALP peptide in DPPC) In your tutorial How many Number of Water Molecules you

Re: [gmx-users] Type 9 dihedral in Gromacs topology

2012-10-27 Thread Peter C. Lai
On 2012-10-27 01:20:15PM -0400, Andrew DeYoung wrote: > (1) What is a type 9 dihedral? On page 74 of Section 4.2.12 of the manual, > it says, "For certain force fields, type 9 is useful. Type 9 allows > multiple potential functions to be applied automatically to a single > dihedral in the [ dihed

[gmx-users] Type 9 dihedral in Gromacs topology

2012-10-27 Thread Andrew DeYoung
Hi, This question is a sequel of sorts to my earlier question about dihedral parameters in Gromacs (http://lists.gromacs.org/pipermail/gmx-users/2012-October/075860.html). I typically use the OPLS-AA force field. In OPLS-AA, dihedrals are usually specified with the Ryckaert-Bellemans function.

Re: 回复： 回复： [gmx-users] ATP/ADP+Pi

2012-10-27 Thread João M . Damas
Perhaps I was not too explicit. The parameterization details are on the first supplementary information file of the first paper I sent you. Here is the direct link: http://pubs.acs.org/doi/suppl/10.1021/jp905735y/suppl_file/jp905735y_si_001.pdf The parameters are built upon the already available A

Re: [gmx-users] Conceptual question about the representation of dihedral angles in Gromacs

2012-10-27 Thread Arman Mahboubi Soufiani
Dear Andrew, I am a beginner! However, I would like to record my interpretation of the concept you're confused about and evaluate it by what experts will comment later. I am pretty sure your first calculation of 2,7 kcal/mol is correct, however, since ethane is symmetrical molecule you don't need

Re: [gmx-users] Conceptual question about the representation of dihedral angles in Gromacs

2012-10-27 Thread David van der Spoel
On 2012-10-27 03:02, Andrew DeYoung wrote: Hi, If you have time, may I ask a conceptual question about how dihedral angles are specified in force fields? Consider ethane, a two-carbon hydrocarbon (H_3C-CH_3). It has two carbon atoms and six hydrogen atoms. Call the carbons C1 and C2. Hydroge

[gmx-users] About Solvation of Lipid Protein

2012-10-27 Thread vidhya sankar
Dear Justin Thank you for your Previous reply I am  following your Protein-lipid Tutorial ( KALP peptide in DPPC) In your tutorial   How many   Number of Water Molecules  you  needed   to  solvate Lipid -protein  Wh