Re: [AMBER] An error during NPT/production (GPU run)

From: Женя Елизарова <>
Date: Sat, 28 Nov 2020 11:10:09 +0300

I see. I have sent you files. This letter awaits moderator approval because
the message body is too big.
Our system consists of 63420 atoms.

I also would like to ask some more questions. Which performance you suppose
sould be for such size of the system on GPU? (for example in ns/day). So I
could understand is everything alright with the installation.
Another question is about calculations in a vacuum. Is it possible on GPU?
If so, could you help me and tell me what I need to do? (how to make a box
or I don't need it, which parameters I need to change in input files).

Thank you in advance!

Evgenia Elizarova

пт, 27 нояб. 2020 г. в 16:04, David A Case <>:

> On Thu, Nov 26, 2020, Женя Елизарова wrote:
> >
> >We also checked the size of our
> >system. It is smaller than the possible size (here you write some
> >limitations of possible calculations....)
> How big is your system? The GPU code can indeed fail in odd ways for
> small systems, but that is supposed to be checked for at the beginning.
> What is it exactly that makes you think your system is too small?
> You might see if adding more water (to make the box sizes bigger than 30
> Å or so) has any effect. But I'm just guessing here, based on your
> comments. You may need to post files that would allow others to try to
> reproduce the problem.
> ....good luck....dac
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Received on Sat Nov 28 2020 - 00:30:02 PST
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