<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Respectable David/Justin/Mark/Berk</DIV>
<DIV>In my study of diffusion of oxygen in water, I solved the segmentation fault problem as below</DIV>
<DIV>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</DIV>
<DIV>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.</DIV>
<DIV>3 I than ran again for 500 ps using the same technique.</DIV>
<DIV>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.</DIV>
<DIV> </DIV>
<DIV>Now the run upto 100 ns went without any segmentation fault.</DIV>
<DIV>Is this the way I should solve the problem?</DIV>
<DIV> </DIV>
<DIV>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).</DIV>
<DIV>Actually, as the time increases it increases, Why is this happening?</DIV>
<DIV>We are doubtful about the force field parameters we have supplied. </DIV>
<DIV>Specially, the nonbonded parameters.</DIV>
<DIV> </DIV>
<DIV>I have tried to define bare oxygen in .atp file </DIV>
<DIV>Is not that the charge of bare oxygen is zero?</DIV>
<DIV> </DIV>
<DIV>Could you tell me what is the value for nonbonded parameters for oxygen molecule and spc water molecule? </DIV>
<DIV>OB--------OW</DIV>
<DIV>OB---------HW</DIV>
<DIV> </DIV>
<DIV>In the nb.itp the nonbonded parameter (Linard-Jonnes) between oxygen and water hydrogen is given as zero.</DIV>
<DIV>I am stuck at this step and I need to solve it anyway for my Msc. Thesis. Please help me.</DIV>
<DIV> </DIV>
<DIV> </DIV></td></tr></table><br>