Re: [gmx-users] Trajectory optimization - 2 chains are separated

2020-02-15 Thread Marwa Abd El Kader
Dear Justin, I 've tried centering on one chain and the same problem still exists, any suggestions? On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul wrote: > > > On 2/14/20 2:48 AM, Marwa Abd El Kader wrote: > > Dear Justin, > > Would you please tell me how, give me an exam

Re: [gmx-users] Trajectory optimization - 2 chains are separated

2020-02-13 Thread Marwa Abd El Kader
Dear Justin, Would you please tell me how, give me an example code, because I'm a novice? Thanks in advance, Marwa On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote: > > > On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: > > Dear gmx-users mailing list team, > > I wa

[gmx-users] Trajectory optimization - 2 chains are separated

2020-02-13 Thread Marwa Abd El Kader
Dear gmx-users mailing list team, I want to know how to fix the separation of 2 chains after the production run. I'm trying different combinations of trjconv after creating an index file having a specific residue(s) on the interface between the 2 chains, but nothing is working. I fixed this issue