[gmx-users] continuation run in parallel with shuffle and sort option

[chris.neale at utoronto.ca]

> Thanks a lot for your suggestion. I wanted to calculate lateral
> diffusion co-efficient for lipid, so it needs a long run. I understand
> I should give more time on making
> this working. I have already downloaded g_desort.c, and was successful
> upto some steps, but not the whole. If I get doubts further, can I ask
> you?

You can certainly post a question to the list. You will need to be  
very specific as you outline any problem that you have, and while you  
are likely to get an answer there is never that guarantee. However,  
note that gromacs 4 is on its way and the entire g_desort procedure  
will be useless then (domain decomposition will take care of all of  
that seamlessly). Therefore I suggest that you just start your run  
without either -shuffle or -sort. Then you can try to get the g_desort  
method working on a test version of your lipid and introduce the  
method to the regular production run when it's ready. In this way you  
shouldn't loose any time. For example if you spend the next week  
setting up g_desort then it is possible that it would have been faster  
overall just to start immediately.

Chris.