Re: [gmx-users] setting vdw cutoff with specific force-filed?

Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS

Re: [gmx-users] setting vdw cutoff with specific force-filed?

On 04/08/11, Justin A. Lemkul jalem...@vt.edu wrote: Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on

Re: [gmx-users] setting vdw cutoff with specific force-filed?

Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van der Waals Parameters) to calculate non-bonded vdw interactions that are not between third neighbors, such as CH1 carbons between different chains in a biomolecular system. Anything wrong here? I understand

Re: [gmx-users] setting vdw cutoff with specific force-filed?

Yun Shi wrote: Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van der Waals Parameters) to calculate non-bonded vdw interactions that are not between third neighbors, such as CH1 carbons between different chains in a biomolecular system. Anything wrong

[gmx-users] setting vdw cutoff with specific force-filed?

Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper *A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets