how to rerun a namd trajectory in order to complement the missing snapshots?

From: sunyeping (
Date: Thu Aug 18 2016 - 22:35:51 CDT

Dear all,
I guess I missed some important snapshots which contains important atom interaction information for understanding a conformational transition in a namd run because I set a low output frequency. It is possible to rerun a certain fragment of the trajectory with a higher output trajectory so that the new output trajectory contains all the original snapshots of that trajectory fragment but complemented with the snapshots between them.     Maybe it is impossible to reproduce exactly the original trajectory. My aim is to understand how the molecule transforms from conformation A in snapshot A to conformation B in snapshot B. If I cannot rerun the trajectory form snapshot A to snapshot B in a normal MD,  maybe I can use target MD to do it. But I guess the conformational transition is caused by the internal atom interaction in the molecule, so would target MD -- which adds an extra force to the molecule -- be useful ?

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