[gmx-users] Bug (?) with FEP while using particle decomposition in charge transformation

0 1.83755 0.183755 0.3200 3.91737 0.391783 0.3400 5.79081 0.579126 0.3600 4.92766 0.492766 0.3800 8.06557 0.806605 0.4000 7.00964 0.700994 0.4200 12.1488 1.21481 So the signs of the dH/dlambda are opposite while using particle decomposition. There is no such problem while running VdW transformat

[gmx-users] Domain decomposition in FEP

91   2.791   3.426   3.184   640LIG    C18 4392   2.834   3.453   2.937 and the actual distance is 1.55 A - quite OK for single C-C bond. And another interesting fact is that it doesn't occur during FEP calculation of the same system without soft-core and aimed at only charge perturbation. I

[gmx-users] Fw: Normal mode analysis

How can I obtain normal frequencies and normal modes? How are normal frequencies and normal modes connected with eigenvalues and eigenvectors? Calculation of the system of 3000 atoms with g_nmeig gives 3000 eigenvectors which consists of 3000 coords instead of 9000*9000, why? _

[gmx-users] Fw: Amber to OPLS

Is there any tool to create OPLS topology or obtain charges or is there any library of such topologies (compound of interest: BCL (bacteriochlorophyll) and lycopene? Can I use charges from Amber in OPLS? Thanks in advance. ___ gmx-users mailing list

[gmx-users] Double precision gives infinite force while single doesn't

-4.0 and i always have this problem. Maybe there's some hints for compiling double precision version in Mandriva 2008? Thank you, Alexey Zeifman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl