Hi gromacs users, I am running TEE-REX calculations on a tetrameric protein with 3 replicas and I have come up several problems. I have calculated the principal components of a 6 ns molecular dynamics. The temperature of the essential subspace (T_es) in these replicas are 300, 400 and 650K (tau_es = 0.05 ps), whereas the rest of the system is at 300K (coupling constant of 0.1 ps).
1) T_es fluctuates in a huge range of temperatures (100-800K in the replica at 400K and 200-1200K in the 3rd replica). I have read in the T-Rex README file that the fluctuations of T_es are likely to be greater than the temperature of the rest of the system but not greater than 40K, so the problem is really serious. I cannot reduce these ranges by reducing the coupling constant to 0.04 ps or by using a different essential subspace. 2) This problem gets worse when I do the same calculation with a bigger tetrameric protein. T_es gets aberrant values such as 20397713408 K. Indeed, the T-Rex simulation of this protein required bigger tau_es values to begin the simulation. If not, only the replica at 650 K stopped at the first steps as a result of a huge separation between adjacent atoms (system exploding warning). BTW, a traditional MD at 650K has a normal behaviour. Thanks in advance, Ramon _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
