AMBER Archive (2005)

Subject: AMBER: serial and parallel

From: Aknb (bahiyahn_at_tm.net.my)
Date: Sun Apr 24 2005 - 06:35:37 CDT

Dear Amber Users,

i have two questions to ask and really hope to get some feedbacks from all of you

1) is it okay to combine serial and parallel runs together? i mean, for example, i did 20 ns of simulation in serial and from 21-40 ns was later done in parallel for the same system. it's not consistent, but will that leads to faulty results?

2) my second question is regarding the MM-PB/GBSA calculation, is there any hard rules for the input to be trajectories collected from explicit solvent simulation? can i use trajectories collected from in vacuo simulation as an input for MM-PB/GBSA?

thank you very much in advance

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