Re: [AMBER] doubt frames simulation

From: David A Case <>
Date: Sat, 2 Jan 2021 08:55:59 -0500

On Sat, Jan 02, 2021, MYRIAN TORRES RICO wrote:
>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...

Examine the mdout files for these runs: are there any indications that the
runs didn't finish properly?

Try a cpptraj run with just your trajin command and nothing else. Do this
for both the file that gives 11873 and the one that gives 39000. Read the
cpptraj output *very* carefully. Are there any hints there? (Both values
are incorrect, given the information you have provided.)

Run a short simulation, say with 40 thousand steps rather than 40 million.
See if cpptraj is happy with that, and finds 40 frames.


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Received on Sat Jan 02 2021 - 06:00:03 PST
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