Hi Vasya, Glad to hear from you here! I did not work with -rerun yet - it's a useful option I see now.
On Mon, Jul 20, 2009 at 5:39 PM, Vasilii Artyukhov <[email protected]>wrote: > > > 2009/7/20 Vitaly V. Chaban <[email protected]> > >> Hi Matteus, >> >> Yeah, dynamic groups would be a powerfull tool. But such mechanism is >> still under development if I am not out-of-time. >> >> The possible way to proceed with such kind of research (as Berk advised me >> here long ago) is to sort the trajectory (trjorder) based on the distance >> criteria. Then you can make an index file with N first numbers (which are >> close to the protein) and use g_energy with this group and protein group. It >> seems for your task this way is a perfect solution. >> > > Or better yet, use mdrun -rerun on your reordered trajectory and _then_ use > g_energy? This way you would be free of any problems with molecules going in > and out of your solvation shell, if I am getting things right. > -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: [email protected],[email protected] skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html =================================== !!! Looking for a postdoctoral position !!! ===================================
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