[gmx-users] trjcat

Dear GMX users i ve simulated a system with 1500 steps in md.mdp file and every 3000 steps save the coordinations, thus we have 5000 frames i know i should use *trjcat* for reduce my frames, but i dont know how? for instance for reduction to 500 frames, please guide me about that regards --

[gmx-users] trjcat

Dear Thomas i really apprciate for your advice in trjconv -dt NEW_TIME_STEP_IN_ps. you mean place my new time and my new steps of simulation instead of for example 1500 steps please clarify your mean how i can resolve my problem for changing my steps from 15milion steps (5000frame) to 500

Re: [gmx-users] trjcat

Hi Elham, use trjconv -dt NEW_TIME_STEP_IN_ps. Happy simulating, Thomas. -- R. Thomas Ullmann, PhD Theoretical & Computational Biophysics Max Planck Institute for Biophysical

[gmx-users] initial structure generation for performing MD simulations

Hi all, Is there any way to insert a 12 nt DNA inside a 15x15 single wall carbon nanotube using some scripts in VMD or some tools like Packmol? I want to study the displacement of nucleic acids from the core of a CNT at different conditions (temperature, solvent or incrporation of fillers).

[gmx-users] GPU+CPU

Hello Everyone, I recently started to explore GROMACS (switching over from AMBER) and need some help understanding how to launch GPU+CPU simulations. GROMACS 5.0.6 was compiled with the following cmake arguments: cmake .. -DGMX_BUILD_OWN_FFTW=ON

Re: [gmx-users] initial structure generation for performing MD simulations

Hi Soumadwip, ssDNA or dsDNA? There are scripts for building both. I have one for ssDNA that might be suitable for your purpose. You can contact me off-list if you're interested. Cheers, Tsjerk On Sun, Sep 20, 2015 at 5:56 PM, soumadwip ghosh wrote: > Hi all, >

Re: [gmx-users] trjcat

On 9/20/15 4:18 PM, elham tazikeh wrote: Dear Thomas i really apprciate for your advice in trjconv -dt NEW_TIME_STEP_IN_ps. you mean place my new time and my new steps of simulation instead of for example 1500 steps please clarify your mean how i can resolve my problem for changing my