[gmx-users] About Potential energy calculation

Hi all I am doing an NVE simulation of a protein immersed in water, and I want to keep track of the potential energy in the protein. Do you know how can I do it?. I tried saving the energy of the protein ( the protein as an energy group) in the .edr file, but when I checked the file with g_en

[gmx-users] Problem with the simulation of C2160 (fullerene)

Hi guys I have a problem with the MD simulation of C2160 (Fullerene) with doxorubicin molecules inside. I have a OPLS force field for C60 that I am using for C2160, and for Doxorubicin, I generate the force field using PRODRG. The problem is that PRODRG is based on Gromacs so the two structures a

[gmx-users] About Temperature coupling and Energy Transfer....

Hi all. I am trying to simulate a protein initially at 0K in water at 310K. I couple the water to 310K with tc=0.5 and the Protein is decouple tc=-1. The idea is analyze how is the transfer of energy from the water to the protein. The interesting thing is that after 200ps the temperature of the

[gmx-users] About force field for CNT and Lonsdaleite

Dear Friends Does any of you know where can I obtain a FF for simulation of CNT and Lonsdaleite solvated in water, that also contain parameters for N, H, O, P, Cl and F. Thanks John Michael Espinosa-Duran Electronics Engineer. M.Eng. Universidad del Valle. Cali, Colombia, South America.