Thank you for the prompt reply. Just to make sure that i don’t have a bad contact, I explicitly checked all the position (polymer) and the water molecules are at least 2A far away . Thus I don’t see there is direct overlap of the atoms. I am using the box as periodic, which i am not sure causes(leads) to this problem. I have tried various configuration and if there is no overlap at the beginning i think the minimization should go straight forward(as per my knowledge). I am doing the similar simulation with the PEO in water and I am able to simulate NPT simulation at 1femtoseconds and even after running 1ns, i see the negative pressure and if I try to go beyond 1fs(from 1 fs to 2 fs) I see the simulation blowing up. I am not sure how do people make good starting configuration.(any suggestions?)
Thank you for the prompt reply. Just to make sure that i don’t have a bad contact, I explicitly checked all the position (polymer) and the water molecules are at least 2A far away . Thus I don’t see there is direct overlap of the atoms.
Plain visualization is prone to miss things.
I am using the box as periodic, which i am not sure causes(leads) to this problem.
Whether you have overlap across the periodic boundary or not can be verified by the compute rdf command to generate a radial distribution function.
I have tried various configuration and if there is no overlap at the beginning i think the minimization should go straight forward(as per my knowledge).
Right, if there is overlap then in addition to minimization failures you will also see huge positive energy. Unfortunately, your system does have atoms that are within 0.0927 angstroms with other atoms (i.e. overlap), which is verified by RDF.
You will have to fix this overlap first. A good indication is a good, negative energy.
Ray
Hi,
Try to use Packmol software, it will help you.