I have been trying to minimize and relax a long chain molecule, about 80 nm long using amber in implicit solvent using pmemd.cuda. Although, the temperature of my system remains infinity not allowing any further steps of mdrun to continue without any errors. Could anyone please help me with this and explain why the temperature remains infinite and what should be done to get around it.
Kind regards.
Infinite temperature would suggest that initialized velocities are too large. Another issue can be that atoms are very close to each other. This would lead to large repulsion and large increase in particle velocity.
Subhamoy Mahajan, Thank you for the information, but can you suggest how to solve this? The protein i am trying to simulate is indeed pretty large, around 100nm long. The molecules are not very close to earch other, i have visualised the structures.
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