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

[Thompson, Matthew White]

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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