[gmx-users] Analyzing Desmond trajectories using GROMACS tools

[zeineb SI CHAIB]

Dear Justin,

Thank you very much for your help and clarifications.

I have a question please:

I used OPLS-3 force field when running my simulations with Desmond, which is absent in GROMACS 5.1.3
In order to generate the topology (protein and POPC), I guess I have to work with the same force field in GROMACS, OPLS-3.

There is differences between OPLS3 and the OPLS that is implemented in GROMACS and I'm wondering if I can choose the latter when generating the topology and the rtp file for the analysis of my trajectories. May I have your opinion please?


Thank you in advance for your help.


Best regards.


Zeineb