[gmx-users] forcefield

Hi, I want to do simulation with the ligand called zebularine. I dont find forcefied for that. Also i read prodgr has been deprecated.. Could you please help me to find out the forcefield for the ligand zebularine. Thanks in advance lalitha

[gmx-users] regarding visualizing the output

hello sir, 1.i ran simulation for 2 ns.i want to view the structure from 1500 to 2000 frames at every 25 ps.how to get it in pdb strucutres of the above wanted frames. 2.with the use of trjconv i had one pdb file converted from one frame. i'm viewing that structure with VMD, but when

[gmx-users] freeenergy calculation

i have completed my simulation.i want to analyse my protein.can u help me how to calculate the free binding energy calculation,which program i should use.i've read gromacs manual 3.3 but i'm in need of any other new analysis are included in version 3.3 or not.so where can i getthe information

[gmx-users] (no subject)

Dear sir, i'm a new user of gromacs.i've done the installation correctly.while simulating my protein i encounter some of the problems.please give me ur suggetions or any reference to overcome this problem.this is my first experience of running the gromacs.kindly look for my problems