[gmx-users] energy minimization error

[sameer varma]

At 02:54 PM 9/24/2004 -0500, you wrote:




>Hello everyone,
>       I have two questions.
>When I was doing Energy minimization over a system with dppc bilayer(96
>dppc molecules on each layer) and water on either side of the monolayer.I
>was getting an error as follows:
>
>Steepest Descent:
>    Tolerance (Fmax)   =   1.00000e+01
>    Number of steps    =      25,000
>Fatal error:  ci=-2147483648 should be in  0..2159 [FILE nsgrid.c,  LINE
>218]
>
>Can anyone guess where the mistake might be.
>
>My second question is:
>
>When I am trying to do energy minimization only on DPPC bilayer with 96
>molecules in each monolayer what happened is the two monolayers
>flipped.Intially when I created a bilayer the tails of each layer were
>pointing inside but after energy minimization the heads came together and
>tails turned towards the other side.I do not know why it happened like
>that,It did run for 64 and 48 bilayer.It gives problem only with 96
>molecules.
>
>Is there any guess why its happening like this?

It seems like all your lipid molecules are not inside the simulation box, 
which is defined by the dimensions given at the end of the XX.gro file. And 
if have not specifically turned off the periodic boundary conditions for 
energy minimization, the output XX.gro file might be containing a 
collection of lipid molecules from several periodic boxes.

sameer.

>Any suggestions would be greatly appreciated.............
>
>Thanking you,
>Dinesh.
>
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