Dear all,
I'm running simulations on membrane proteins (POPC) using Desmond software and I would like to use GROMACS tools to analyze certain parameters related to the membrane. Exemple:
- Deuterium order parameters of the acyl chains
- Density of the membrane environment
- Area per lipid headgroup
- Bilayer thickness
- Lateral diffusion of the lipids
Some files are easy to generate using VMD (.trr, .gro files) but I'm having difficulties to generate a tpr file.
Could you help me with any available tools please.
Thank you in advance for your help.
Zeineb
Dear Stéphan,
Thank you very much for your response which is very clear!
May I have your opinion concerning this point 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 of my system in GROMACS (protein and POPC), I have to work with the same force field: 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?
Thank you in advance for your help.
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