How to deal with trajectories from RAMD in NAMD?

From: 王伊秋 (wangyiqiu08_at_126.com)
Date: Thu May 27 2021 - 20:54:58 CDT

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 Dear all:
 
    I recently have used RAMD in NAMD developed by your group once.I lack experience of RAMD.Now I meet some problems.

    In my system,there are two ligands that are bonded by hydrogen bond.They are not burred at the protein but only are bonded by hydrogen bond. I hope one of them will be pulled,another ligand still stays bound with the protein.But two abnormal cases may happen:
     

  1) Two ligands may be pulled together.

  2) The ligand that I hope be pulled may be not pulled but the simulations is terminated when the distance between the COM of ligand and the COM of protein reaches the max distance set in the conf file.

  I don't know why two cases above happen.On the basis of the two cases above, I think I may watch trajectories one by one by using visualization software.However,this is a challenging task.Do you have a better way?

  Best wishes,

  Cynthia

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