Re: [gmx-users] Linear CG beads, grompp doesn't work

2013-01-02 Thread XAvier Periole
I think your original problem is that you define only one charge group for the entire molecule/polymer. You need to define each bead in a separate charge group and things will be fine :)) you do not have charges anyways. As far as I know angles have never made martini unstable but the

[gmx-users] Linear CG beads, grompp doesn't work

2013-01-01 Thread Xu Dong Huang
Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there

Re: [gmx-users] Linear CG beads, grompp doesn't work

2013-01-01 Thread Justin Lemkul
On 1/1/13 10:33 PM, Xu Dong Huang wrote: Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same

Re: [gmx-users] Linear CG beads, grompp doesn't work

2013-01-01 Thread Xu Dong Huang
Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. Xu Dong

Re: [gmx-users] Linear CG beads, grompp doesn't work

2013-01-01 Thread Justin Lemkul
On 1/1/13 10:46 PM, Xu Dong Huang wrote: Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and

Re: [gmx-users] Linear CG beads, grompp doesn't work

2013-01-01 Thread Xu Dong Huang
@Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at

Re: [gmx-users] Linear CG beads, grompp doesn't work

2013-01-01 Thread Justin Lemkul
On 1/1/13 10:51 PM, Xu Dong Huang wrote: @Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) Presumably. As long as you satisfy the criteria mentioned in the tutorial (moment