Hi,I am trying to NVT equilibrate without constraints after NPT simulation with constraints. but i am getting the errors in tau_t and many more. can anyone suggest what is wrong with the mdp file.
Martin Klvana
Warning:The bond in molecule-type Protein_chain_C between atoms 185 OG1 and 186
HG1 has an estimated oscillational period of 9.0e-03 ps, which is less
than 5 times the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Constraints allow you to use a longer time step, so if you're turning them off, then naturally you have to decrease the time step down to 1 or 0.5 fs. I don't see what the point is in turning off constraints but maintaining position restraints.
The errors related to tau_t are due to the fact that you're specifying two groups for temperature coupling but then only providing one set of parameters (tau_t and ref_t). Looks like you're taking files from my tutorials and modifying them, so go back to the correct tutorial files to fix your mistakes.
Justin Lemkul Thank you for pointing out the error. yes, you are right, your tutorials are the foundation documents for performing simulation for beginners like me. I got your point.
But i do have one more question, i was trying to redo some calculations from a paper only to found out if i am proceeding correctly.
in that paper, the author performed NPT position restrained simulation in the first step, then NVT equilibration without restraints. so i mean to ask how to remove position restraints from the file you have in your tutorials for NVT equilibration only not simulation?
THanks in anticipation!!!
Article From Proteins to Perturbed Hamiltonians: A Suite of Tutorial...
See section 3.2.5, pages 10-11.
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