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.
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