Re: [gmx-users] kind of contacts in protein-dna interaction during simulation

On 7/11/2010 9:36 PM, leila karami wrote: Dear Mark thanks for your attention. I read manual before. I know that g_hbond is for hydrogen bond analysis. But I don’t know about Van der Waals interactions analysis and how to obtain percentage of them. If you're planning to copy someone else'

[gmx-users] kind of contacts in protein-dna interaction during simulation

Dear Mark thanks for your attention. I read manual before. I know that g_hbond is for hydrogen bond analysis. But I don’t know about Van der Waals interactions analysis and how to obtain percentage of them. Please give me more information about what I said. -- Leila Karami Ph.D. student of

Re: [gmx-users] kind of contacts in protein-dna interaction during simulation

On 7/11/2010 8:02 PM, leila karami wrote: Hi gromacs users In following article, in table 2, author brings Protein–DNA contacts observed in the simulation. I want to know how to obtain 1) Van der Waals interactions 2) percentage of population regarding Direct hydrogen bond, Van der Waals a

[gmx-users] kind of contacts in protein-dna interaction during simulation

Hi gromacs users In following article, in table 2, author brings Protein–DNA contacts observed in the simulation. I want to know how to obtain 1) Van der Waals interactions 2) percentage of population regarding Direct hydrogen bond, Van der Waals and Water-mediated hydrogen bond. In method sect