[gmx-users] Re: fullerene topology

I forgot to ask if there is a forcefield for gromacs that will handle fullerenes. Is there? -Adam On Dec 5, 2007 1:17 PM, Adam Fraser [EMAIL PROTECTED] wrote: I'm trying to either build or find topology files for buckminster fullerene (C60). Does anyone know where I could find such files

[gmx-users] fullerene topology

I'm trying to either build or find topology files for buckminster fullerene (C60). Does anyone know where I could find such files? If not, does anyone know of literature that would help me build C60? I already have a pdb of the structure... I just need accurate partial charges to build the

Re: [gmx-users] applying force and fixing atoms in gromacs

Ah, groovy, I was clearly using the wrong search terms, and didn't make the connection when I was looking through the contents. Cheers -Adam On 10/19/07, Mark Abraham [EMAIL PROTECTED] wrote: Adam Fraser wrote: Hello, I was looking in the manual for how to fix atoms and apply constant

[gmx-users] applying force and fixing atoms in gromacs

Hello, I was looking in the manual for how to fix atoms and apply constant (or time dependent) force to atoms. Could someone please help me get started with this? Thank you, Adam ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] stuck

Hello, I'm trying to get started working with a system of 2 hexadecane molecules in water but I'm having some trouble. I'm getting the following error when I run: grompp -f simulate.mdp -c 2Hex_solv.gro -p 2Hex.top -o md.tpr Program grompp, VERSION 3.3.2 Source code file: readir.c, line: 794

[gmx-users] simulating hydrocarbons in water

Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built

Re: [gmx-users] simulating hydrocarbons in water

that converts pdb to gro, and I still get the above error. -Adam On 10/10/07, David van der Spoel [EMAIL PROTECTED] wrote: Adam Fraser wrote: Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've

Re: [gmx-users] simulating hydrocarbons in water

Much appreciated, works beautifully! On 10/10/07, TJ Piggot [EMAIL PROTECTED] wrote: Just as a note editconf will covert a pdb to a gro file Tom --On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser [EMAIL PROTECTED] wrote: Yes I tried this and it doesn't work for me. I get

Re: [gmx-users] simulating hydrocarbons in water

PROTECTED] wrote: Adam Fraser wrote: Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) did you use 3.3.2 ? The default

[gmx-users] simulating Hexadecane in water

Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I have built