[gmx-users] Re:Re: g_order in GROMACS 3.3.2 and 3.3.1

Dear all GROMACS user : After generating the .ndx file which contained only one group that one tail of DPPC, I use g_order to calculate order parameters. But there are nothing in deuter.xvg and order.xvg file. The process is listed below: step1: make_ndx -f XXX.pdb -o index.ndx

[gmx-users] g_order in GROMACS 3.3.2 and 3.3.1

Hello, gmx developer and users: After modifying the source code of g_order in GROMACS 3.3.1 with Bug #84 and compiling again, I got the error message when using g_order to calculate order parameteters of POPC bilayer. The error message is : grp 1 does not have same number of elements

[gmx-users] Re : Positive and negative ions move in the same direction under a constant electric field?

Dear Mark and Tom： Thanks for your answer. In order to modify the term of temperature coupling group, I chose “system” in place of “SOL” when using the genion function. So the temperature coupling in .mdp file became： tc_grps=System tau_t =0.1 ref_t =300 I chang

[gmx-users] Positive and negative ions move in the same direction under a constant electric field?

Dear all： In order to make sure that my procedure for applying electric field using Gromacs is correct, I applied electric fields to sodium chloride solvent (SPC216.pdb with NA+ and CL-) in the x direction. After 2 ns running, the trajectories of ions and water molecules showed that both