Re: [gmx-users] how to visualize gromacs trajectory

give me some examples of the command for each step? > > Thanks. > > Yeping > > ---------- > > From:孙业平 > Sent At:2019 Jul. 3 (Wed.) 17:39 > To:gromacs > Subject:Re: [gmx-users] how to visualize gromacs trajectory > > Hi, Steph > > I used the following command

Re: [gmx-users] how to visualize gromacs trajectory

Subject:Re: [gmx-users] how to visualize gromacs trajectory Hi, Steph I used the following command to repair the trajectory: gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center -pbc mol -ur compact the bond stretching has disappeared, but the subunits of the protein seperate from

Re: [gmx-users] how to visualize gromacs trajectory

On 7/3/19 5:27 AM, sunyeping wrote: Hi, Steph I used the following command to repair the trajectory: gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center -pbc mol -ur compact the bond stretching has disappeared, but the subunits of the protein seperate from each

Re: [gmx-users] how to visualize gromacs trajectory

it be useful to repeat the trjconv command? Yeping -- From:Stephani Macalino Sent At:2019 Jul. 3 (Wed.) 12:24 To:gromacs Subject:Re: [gmx-users] how to visualize gromacs trajectory Hello, It sounds like you have to fixed broken molecules

Re: [gmx-users] how to visualize gromacs trajectory

-- From:孙业平 Sent At:2019 Jul. 3 (Wed.) 17:27 To:gromacs Subject:Re: [gmx-users] how to visualize gromacs trajectory Hi, Steph I used the following command to repair the trajectory: gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o

Re: [gmx-users] how to visualize gromacs trajectory

Use “dynamic bonding” option from VMD, you can access it by vmd >> graphics >> representations >> drawing method >> choose DynamicBonds.Other way is make trajectory whole at every time stamp.RunGmx trjconv -f input.gro -o output.gro -s input.tpr -pbc mol Gmx

Re: [gmx-users] how to visualize gromacs trajectory

Hello, It sounds like you have to fixed broken molecules and have problem with boundary conditions. After doing the MD, you need to fix your trajectory first before doing visualization. Check this link for a workflow: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

[gmx-users] how to visualize gromacs trajectory

Dear all, I wish to know what is the best way to visualize gromacs trajectory. When I load a gromacs trajectory into VMD, I find some of the water molecules and some part of the protein in the system are streched and the structure become weild and cannot be properly analyzed. I searched google