[gmx-users] Question: KALP-15 in DPPC tutorial

[Tapash, Arifuzzaman]

Hi all,

I'm very new in Gromacs. I have completed the Lysozyme in water tutorial (by Justin A. Lemkul) successfully. Now I'm doing the KALP-15 in DPPC. 

I have successfully done the equilibration stage (both temperature and pressure). I have a question about the npt.trr file. 

After completing the pressure equilibration, the npt.trr file was generated which is about 17 GB size, provided the equilibration was done for 1 ns (I used all the *.mdp file provided there, didn't do any change) and I followed all the procedure mentioned in the tutotial. During the solvation process I used 1.0 nm distance of box side (gmx editconf -f *.gro -o *.gro -c -d 1.0 -bt cubic).

1) My question is, is the file size (17 GB - npt.trr) normal? Or I did any mistake during previous steps?

I am concerned because, the cluster I'm using, they provide only 25 GB space. So, if for some reason, I have to do the equilibration for longer time, it will produce a bigger file. 


2) My another concern is, will the 'Production MD' step will produce a very large file (larger than 25 GB)?

I'm sorry, these might be very silly question, and I know all of you are very busy with your work. 

Thanks for taking time to help me. 

Arifuzzaman Tapash