[gmx-users] (no subject)

Sunil Thapa mephysik at yahoo.com
Mon Mar 2 07:43:45 CET 2009

Respectable David/Justin/Mark/Berk
In my study of diffusion of oxygen in water, I solved the segmentation fault problem as below
1. At first I ran for 16 ps beyond which segmentation fault occured in the previous run. I generated the .gro file of that run
2. I then ran for 100 ps using the .gro file of step 1. Also generated the .gro file from this step. I constantly checked the pressure content. It really decreased from 4000's to 1400s. No segmentation fault occurred.
3 I than ran again for 500 ps using the same technique.
4. When I ran for 1 ns, there was no segmentation fault as well as the pressure was about 1 bar which I needed. The temperature was 298 K as I needed.
Now the run upto 100 ns went without any segmentation fault.
Is this the way I should solve the problem?
Now when I saw the msd curve, it was nearly straight line and the calculation yielded the diffusion coefficient of oxygen as 40000 x 10(-9), where as the experimental value is nearly 2 x 10(-9).
Actually, as the time increases it increases, Why is this happening?
We are doubtful about the force field parameters we have supplied. 
Specially, the nonbonded parameters.
I have tried to define bare oxygen in .atp file 
Is not that the charge of bare oxygen is zero?
Could you tell me what is the value for nonbonded parameters for oxygen molecule and spc water molecule? 
In the nb.itp the nonbonded parameter (Linard-Jonnes) between oxygen and water hydrogen is given as zero.
I am stuck at this step and I need to solve it anyway for my Msc. Thesis. Please help me.

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