Dear Amber users,
I have been trying to do REMD simulation on a 50 a.a peptide following the
A7 Amber tutorial. I am not new to MD simulations but I have been
struggling about some issues.
*First* is now I ran the replicas just as long as the tutorial (500 steps),
how do I know what is the proper length of replicas for my own system? Is
there anyway to calculate? paper? methodology? etc.
*Second* is the md.out files of my replicas, some of my exchanges were
successful and some were failed.As there are no more explanation in the
tutorial, I have problem interpreting the output files. I attached two
examples(failed and successful one here).
*Third* is I have problem visualizing the remed trj files. Just to simply
visualize the system I tried grep -v REMD but couldn’t load it in VMD. I ll
attach the original sander out trajectory and topology file here ( I have
removed it, so that my mail could be posted, will send it back if
necessary)
Will be very grateful if you could help me with these issues.
Best Regards,
Maryam
.
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Received on Fri Nov 27 2015 - 03:00:03 PST
