[gmx-users] Regarding box size and the rlist values

[Mark Abraham]

Hi,

Your model physics sets the minimum box size, and you need to fill it with
stuff so the density will be suitable.

Mark

On Sat, 21 Oct 2017 13:47 Thompson, Matthew White <
matt.thompson at vanderbilt.edu> wrote:

> The error tells you exactly what you need to know. Your box size must be
> twice the cutoff to run (or more likely three times the cutoff to produce
> useful results). Reducing your cut-off usually means your results don't
> properly reflect the force field as it was parameterized and should be
> avoided.
>
> If your box size decreases below a certain size during NPT, simply add
> molecules until the equilibrium box size is large enough. You should be
> able to calculate this from a known/estimated density and target box size.
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Dilip H N
> [cy16f01.dilip at nitk.edu.in]
> Sent: Saturday, October 21, 2017 2:07 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Regarding box size and the rlist values
>
> Hello,
> I am running a simulation of my system of box length 2.1 nm (since i have
> less number of molecules and small molecular size), and i am using
> charmm 36 FF, hence i am using rlist = 1.2 (since these are the parameters
> for charmm FF in the link
>
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FTerminology%2FForce_Fields%2FCHARMM&data=02%7C01%7Cmatt.thompson%40vanderbilt.edu%7Cd3b0376d22704cef53d608d518526505%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636441664542278955&sdata=PxQGay94HkNzjSiibhLhhZXP0k1y60UMRjFTDx1%2BNhk%3D&reserved=0
> ).
> But if i do the compilation for energy minimization (by gmx
> grompp command), i get the following error as:-
>
> "ERROR: The cut-off length is longer than half the shortest box vector or
> longer than the smallest box diagonal element. Increase the box size or
> decrease rlist."
>
> So which is the correct method to solve this..?
> 1] can i change/decrease the rlist (this would violate the charmm FF
> parameters) or
>
> 2] if i increase the box length, it runs fine.
> But after this, if i do nvt followed by npt equilibration, hereafter in
> the npt simulation, the box size decreases, and here, the box size is less
> than rlist, which again gives the same error ("ERROR: The cut-off length is
> longer than half the shortest box vector or longer than the smallest box
> diagonal element. Increase the box size or decrease rlist.")  during
> compilation of production md run.
>
> So what is the correct method/way to overcome this issue...??
>
> Any suggestions are appreciated
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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