[gmx-users] gromacs query for force field in vaccum and liquid

I want to simulate membrane protein in vaccum so let me know which force field i can use for it. Also I m doing simulation for the same protein in liquid using OPLS force field.Please tell me is it correct? -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] gromacs query for force field in vaccum and liquid

On 8/11/2011 8:24 AM, Anushree Tripathi wrote: I want to simulate membrane protein in vaccum so let me know which force field i can use for it. Probably none of them - they were all parametrized on condensed-phase data. In order to do such a simulation, you are going to have to establish a

Re: [gmx-users] Gromacs query for vaccum medium

I have seen different articles on MD simulation in vaccum but i didn't get the exact way for it.If u can tell me the exact way then i can proceed for it fastly because I have to do it within certain time limit. On Thu, Nov 3, 2011 at 11:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On

Re: [gmx-users] Gromacs query for vaccum medium

Anushree Tripathi wrote: I have seen different articles on MD simulation in vaccum but i didn't get the exact way for it.If u can tell me the exact way then i can proceed for it fastly because I have to do it within certain time limit. It would be useful if you were to describe what it is

[gmx-users] Gromacs query for vaccum medium

Let me know how to simulate a membrane protein in vaccum medium by using gromacs commands.What are the basic differences in commands as well as parameters used in liquid and vaccum medium? Please guide me. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Gromacs query for vaccum medium

On 4/11/2011 4:58 AM, Anushree Tripathi wrote: Let me know how to simulate a membrane protein in vaccum medium by using gromacs commands.What are the basic differences in commands as well as parameters used in liquid and vaccum medium? Please guide me. I suggest you do all the GROMACS

[gmx-users] gromacs query

I m using gromacs 4.5.3 version and trying to simulate a protein in liquid media but I found problem in eqilibration step especially when I give following command: mdrun -deffnm nvt .After giving this command it is showing error,i.e., There is no domain decomposition for 4 nodes that is

Re: [gmx-users] gromacs query

Anushree Tripathi wrote: I m using gromacs 4.5.3 version and trying to simulate a protein in liquid media but I found problem in eqilibration step especially when I give following command: mdrun -deffnm nvt .After giving this command it is showing error,i.e., There is no domain