[AMBER] doubt frames simulation

From: MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
Date: Sat, 02 Jan 2021 14:00:50 +0100

Hello again,

Having read all your questions, I am going to summarize my problem
with more information about my simulations:

I think I am using an ascii trajectory format (iwrap = 1), but I have
my doubts because although my final coordinate files are .crd, I use
these later with cpptraj and input for MMPBSA.

On the other hand, the frames that I expect are 40000 (nstlim =
40000000 and ntwx = 1000) and a value of dt = 0.002, but when I
calculate pucker, distances ... it only generates 11873 for example.
But, with other simulations, with the same values ​​of nstlim, ntwx
and dt, they generate 39000 frames in subsequent calculations...

That's why I don't understand why this happens, if I haven't changed anything.

Thanks in advance,


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Received on Sat Jan 02 2021 - 05:30:03 PST
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