Re: [AMBER] tleap/xleap performance enhancement

From: Himanshu Joshi <>
Date: Fri, 7 Feb 2020 11:08:39 -0600

Dear Prof Case,

Thanks for your response, I will appreciate if you can suggest any possible
get around.

There are solutes like DNA, protein and counterions in the system, I am
using parmbsc1 and ff14 for the DNA and protein, tip3p for water model.
However, the time consuming part is the water in the system,

One update, the tleap proceeding becomes even slower as the time
proceeds, contrary to earlier estimate, after 12 hours it has created only
500,000 water
molecules. And now I am concerned that it might be slower towards the end.

Thank you.

On Fri, Feb 7, 2020 at 7:00 AM David A Case <> wrote:

> On Thu, Feb 06, 2020, Himanshu Joshi wrote:
> >
> >Although, I could manage to tweak the pdb file format to get recognized by
> >tleap but the process of generating the topology and coordinate file is
> >slower, (approximately 12 hours for 1 million atoms).
> What force fields are you using? Is this just pure water, or are there
> solutes?
> I've seen behavior that sounds similar, but I'm trying to narrow down
> when it happens. No promises, however, that there will be any easy fix
> or workaround.
> ...dac
> _______________________________________________
> AMBER mailing list

*With Regards,HIMANSHU JOSHI *
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Received on Fri Feb 07 2020 - 09:30:02 PST
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