Re: [gmx-users] fullerene topology

s a hammer, every problem begins to resemble a > nail. > > > -- > *From:* [EMAIL PROTECTED] [mailto: > [EMAIL PROTECTED] *On Behalf Of *Adam Fraser > *Sent:* Thursday, 6 December 2007 5:17 AM > *To:* Discussion list for GROMACS users > *Subject:* [gmx-use

[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

[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 topol

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 ma

[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 http://www.gromacs.or

[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

Re: [gmx-users] simulating hydrocarbons in water

an der Spoel <[EMAIL 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

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: > > > Y

Re: [gmx-users] simulating hydrocarbons in water

cript 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

[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 topolo

[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 topo