<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Respectable Mark/Berk/David</DIV>
<DIV>I am trying to study diffusion of oxygen in water at a constant pressure of 1 bar. </DIV>
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<DIV>My system contains 2 oxygen molecules in 110 water molecules of the box size 1.5 nm</DIV>
<DIV>I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run mdp file.</DIV>
<DIV> </DIV>
<DIV>When I run the production run of 1 ns then I get an warning message as follows and the run terminates. Please try to figure out what might have been wrong.</DIV></DIV>
<DIV> </DIV>
<DIV>Grid: 35 x 35 x 35 cells<BR>WARNING: your box is exploding! (ncells = 42875)<BR> Step Time Lambda<BR> 17200 34.40000 0.00000</DIV>
<DIV> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 1.000000 1 2 1.000000<BR> After LINCS 1.000000 1 2 1.000000</DIV>
<DIV>Fatal error: Can not read/write topologies to file type unknown</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>If I change the LINCS to SHAKE with tau_p=0.5 it goes well but at the last step it gives segmentation fault error. I checked the pdb after energy minimization. The molecules are intact and the energy is well converged.</DIV>
<DIV>If I increase tau_p=2.0, also at this step the error persists.</DIV>
<DIV>My system contains 2 oxygen molecules in 110 water molecules of the box size 1.5 nm</DIV>
<DIV>I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run mdp file. </DIV>
<DIV> </DIV>
<DIV>Your help is a boon</DIV>
<DIV>Sunil<BR></DIV></td></tr></table><br>