[gmx-users] Gigantic boxes

[Sergio Manzetti]

Thanks, that fixed it! 




Sergio Manzetti 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Friday, June 23, 2017 3:49:38 PM 
Subject: Re: [gmx-users] Gigantic boxes 

On 6/23/17 6:20 AM, Sergio Manzetti wrote: 
> Hi, I Have prepared a box, which just grows beyond proportions in order to satisfy grompp complaining about the box being less than the double of rlist, so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the box quickly becomes over 14x14x14. When one visualizes it one can see that the molecule is surrounded by at least 5 Å of waters in all directions, so there is plenty of water in the system. Nevertheless, grompp wants even bigger box, and thus more water. 
> 
> Is this common in MD simulations to run megaboxes for molecules that are virtually disappearing in the large water molecule number? 
> 

No, it's not. Make sure you're specifying your cutoffs in nm, not A. 

-Justin 

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Justin A. Lemkul, Ph.D. 
Ruth L. Kirschstein NRSA Postdoctoral Fellow 

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