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

From: Женя Елизарова <>
Date: Mon, 30 Nov 2020 09:09:24 +0300

Thank you for your answer!

I tried different force fields for protein. It occured that the problem (an
error "cpubuffer..") was with ff19SB force field. Calculations with another
types of force fields (14,99) are more stable. Does it mean that i can't
use that force field? Or maybe you know how to fix it?

 Best regards,
Elizarova Evgenia

вс, 29 нояб. 2020 г., 21:39 David A Case <>:

> On Sat, Nov 28, 2020, Женя Елизарова wrote:
> >I see. I have sent you files. This letter awaits moderator approval
> because
> >the message body is too big.
> You may need to try to create a smaller system to see what fails, or
> consider other alternatives to sharing large files.
> >Our system consists of 63420 atoms.
> I probably need to apoligize here: I read your previous email as
> indicating that you thought your system was too small. But since that
> is not the case, other suggestions I made are not relevant.
> >
> >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).
> You can look at the GPU benchmarks on our web site, and roughtly
> interpolate between results for systems that are smaller and those that
> are larger.
> >Another question is about calculations in a vacuum. Is it possible on GPU?
> Look at igb=6 in the manual. But first, be sure that this is really
> what you want to do. The Amber programs and force fields are not
> designd for vacuum simulations. So be sure that you have a good reason
> for doing this.
> ....dac
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Received on Sun Nov 29 2020 - 22:30:02 PST
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