Re: [AMBER] doubt frames simulation

Date: Sat, 02 Jan 2021 15:01:08 +0100

In effect, I just saw in the mdout that without finishing the
execution time they have gone from one stage to another and they have
needed about 50 hours to complete ...
But why does this happen? There is no error message or anything that
has warned me that the stages have been incomplete ... Could it be due
to lack of space in the cluster?

Thanks a lot

David A Case <> escribió:

> 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.
> ....dac
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Received on Sat Jan 02 2021 - 06:30:03 PST
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