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Joined: Mar 2006
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i am simulating a peptide in a membrane with periodic boundary condition. i wonder if i can save the forces exerted by the membrane (or water) on the peptide (or a sidechain or the backbone) into some file during the simulation? your kind help will be appreciated very much.

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rmv Online Content
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Yes, but some knowledge of Fortran would be required; the USRACM routine in source/charmm/usersb.src allows users to add code that will be executed on every energy call (ENER, MINI, DYNA, ...). The atomic energy and force arrays are passed as args, so a good part of the work is already done.

Otherwise, you can re-calc the forces from stored coords and the same setup as used for the simulation (non-bond, periodic boundary, etc.). Note that for constant P simulations, the unit cell sizes are stored with each coord frame in a trajectory, so that they are updated as each coord set is read.


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