[gmx-users] large charge group
gmx3 at hotmail.com
Wed Nov 19 17:15:24 CET 2008
The charge groups "only" affect the neighbor searching,
which in practice means they affect everything.
In Gromacs atoms in two different charge groups will only interactions
when the center of geometry of the two charge groups is within rlist.
The worst case scenario, which has happend to several people, is:
A molecule with a radius of about 0.5 nm is one charge group.
If the cut-off is 1 nm, two molecules will only really start interacting
when they already overlap.
In 4.0 I put a check on large charge groups.
If you have charge groups of more than 10 atoms, grompp will now
warn you with:
"The largest charge group contains %d atoms.\n"
"Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.\n"
"For efficiency and accuracy, charge group should consist of a few atoms.\n"
"For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.\n",
> Date: Wed, 19 Nov 2008 10:01:01 -0600
> From: sunnytov at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] large charge group
> Hello All
> Recently I have figured out the biggest problem that made my system unstable.
> I have parameterized a molecule pretty similar to octane. A single
> charge group used to be assigned to this molecule. With 1 nm cut-off
> distance for LJ interaction and the direct space for electrostatic
> interaction, the system underwent severe volume fluctuation and at the
> end crashed due to enormously large short range coulomb interaction
> energy. The problem was temporarily resolved by using greater cut-off
> distance such as 1.4 nm. But this fixation was not perfect when I put
> this molecule into more complex system. Regardless of the cut-off
> distance even to 1.8 nm did not solve the problem. The simulation
> always terminated due to large coulomb energy even though no direct
> contact or any weird structure was observed at that snapshot.
> With the help of many experts, I have made a single charge group into
> three smaller charge group, which magically fixed all the problem that
> I have had for almost 2 years. I know that charge group is only used
> for neighbor search. Can anybody tell me how the size of charge group
> can influence the interaction between atoms depending on the
> complexity of the system and cut-off distance??
> Thank you in advance
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