[gmx-users] Re: gmx-users Digest, Vol 38, Issue 14

[M.N. Manoj]

>     This is continuation to my previous mail. I am trying to simulate a
> molecule using mdrun but i am getting errors.
>
> After 2 steps i got
>
>   " Warning: 1-4 interaction between 245 and 251 at distance 1.922 which
> is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation. This usually means your
> system is exploding, if not, you should increase table-extension in your
> mdp file. "
>
> and then finally the program is quitting giving the message.
>
>    "Number of grid cells is zero. Probably the system and box collapsed"
>
> i am unable to sort out the real problem of this.I have tried increasing
> the grid size and also table-extension,but still i am getting the same
> message.
>
> Can someone suggest me where i am going wrong and what is to be done???Is
> this problem because of the compiler???
>
>
Hi Ramya,


I have observed similar problem with another protein. It seems not an issue
with the program, but with the protein. U can try running again after a
short geometry optimization of the protein (eg: minimization with Argus lab
tool). This usually happens for proteins with bad Ramachandran plots. See
that also.

Good luck.

-- 
M.N. MANOJ
PROJECT LEADER - BIOINFORMATICS
VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION
BANGALORE
INDIA
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