Hello dear users,
I am trying to simulate lysozyme in water with REST2. The temperature range I have is 300-500K and the number of replicas is 20. I have attached the mdp file and the data.out file that contains the error message here. My simulation fails after the first swap saying the potential is infinite. I believe my system should be well equilibrated because the .gro file I used to generate .tpr files for REST2 is from a 360-ns regular MD at 300K. I have also took a look at the replicas that fail and found that those who failed were involved in Hamiltonian replica exchange swap. Does anyone have any idea? Thanks in advance!
Regards,
Peiyin Lee
Could you attach your file.top and .gro file to review inconsistences?
Hi, Martiniano Bello ,
Sure, the attachments are the processed.top I used before scaling the potential and the .gro file. Thank you!
Hi,
Your files look good, you should minimize your 360-ns complex before starting new calculations for any steric impediment that is present.
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