Dear Amber user,
I want to study the interactions between protein and ions. I am running a simulation with protein, ions and water and I want to save the trajectories of protein and ions.
I know there is a ntwprt command that can allow Amber to save coordinates from atom number 1 to ntwprt, but however, in the topology, the order of atoms comes from protein, waters, and then ions. I can't use this ntwprt command to save protein and ions only.
I wonder if there is a way to save these two trajectories?
Thanks for any help.
Hi, not saving water can save you a lot more space, but I do not recommend this (unless it is absolutely necessary). MD simulations take quite a long time, and repeating them will be hard. So saving water molecules in trajectory can save a lot more pain down the line.
Regarding your question, I hope you can create a mask that can save only desired molecules excluding water.
Ayaz Anwar
Thanks for your reply. I don't want to save trajectory of water because my system is quite large and saving water may just run out of disk space.
Can you please give me more details about creating a mask and how to apply this?
Thanks in advanced.
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