Re: [AMBER] doubt frames simulation

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Sat, 2 Jan 2021 08:26:24 -0500

did you look at the mdout file and see how long it actually ran? perhaps it
did not complete all of the 40000000 steps.


On Sat, Jan 2, 2021 at 8:01 AM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
wrote:

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