Hi! You can simply calculate the nsteps parameter remembering that the simulation time is determined by the formula:

time (in picoseconds) = nsteps * timestep (in picoseconds)

The most common timestep is 2 femtoseconds (fs), usually specified in ps as 0.002.

So if you need the nsteps for 1000 ns, assuming a timestep of 0.002 ps, use the formula and you'll retrieve nsteps = 500000000.

If your timestep is different, simply adjust the calculation accordingly. Hope this helps!

Thank you for suggestion Davide Pietrafesa

I have another query regarding MMPBSA

I have perform MMPBSA calculation of complex having two hetatoms, NDP and UNK after MDS using gromacs.

Can you suggest me how to perform?

Do the two heteroatoms represent the ligands of your complex? Are they both part of a single structure or are they two separate ligands?

To perform MMPBSA analysis, I suggest using AMBERTools, which you need to install on your computer. Here is the link where you can find instructions on how to perform such an analysis for a protein-ligand complex: https://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.php

In general, you need to convert your trajectory to a format such as DCD or another format readable by AMBER. Additionally, you need to create three files containing, respectively, the entire complex, the receptor, and the ligand (in your case, NDP, UNK or both; depends on what these heteroatoms are for you)

I have performed MD simulation of complex containing two Hetatoms using gromacs charms force field.

they are two separate ligand one is cocrystalized ligand(NDP) and other is small molecule(UNK)

Here, I have generated two topology files for NDP and UNK, and included in topol.top file.