[gmx-users] Re: positive potential energy

[Mark Abraham]

On 29/12/2011 8:24 PM, Zahra M wrote:
> Sorry ...I forget to announce that my potential energy is positive, is 
> it logical?

No.

>
> ------------------------------------------------------------------------
> *From:* Zahra M <s_zahra_mousavi at yahoo.com>
> *To:* "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> *Sent:* Thursday, December 29, 2011 12:52 PM
> *Subject:* positive potential energy
>
> Hi dear all
> I'm simulating a system containing CNT, when I put CNT in a unit cell 
> and want to run energy minimization in a vacuum, I encounter with such 
> an error: "The optimal PME mesh load for parallel simulations is below 
> 0.5   and for highly parallel simulations between 0.25 and 0.33,   for 
> higher performance, increase the cut-off and the PME grid spacing", 
> after running grompp. I've tried a lot of numbers for cut-off radius 
> ,but I didn't get any result, at last I changed the coulomb type from 
> PME to Cut-off, and it worked, I want to know if my results will be 
> reasonable in this case or not, and how to solve that error.

It's not an error, but an advisory about your performance, and doesn't 
matter for EM in vacuo which will only run for a few seconds. Using a 
plain cut-off is unreasonable by definition, but doesn't matter for EM 
in vacuo. Otherwise, you should note that the suggestion is to "increase 
the cut-off *and* the PME grid spacing," not just one of them.

Mark

> thank you in advanced
> Bests
>
> -Zahra
>
>
>
>

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