[gmx-users] PMF calculation

Dear gmx-users Iwould like to calculate the PMF between two nanotubes covered with some molecules. To do that, one nanotube has to be held fixedly and another one  is supposed to be moved as a rigid entity. To generate configurations,  for fixed nanotube  I used position restraints in all

[gmx-users] a program to calculate the adsorbed molecules

Dear gmx users I would like to calculate the number of the surfactant molecules adsorbed on the nanotube surface as a function of time. I would be pleased if anyone could tell me whether there is a program in gromacs to do that or not?   regards -- gmx-users mailing list

[gmx-users] equilibration of the simulated systems

 Dear gmx users would you please tell me how I can be sure that my simulation time is long enough? is it appropriate way to use g_energy program and calculate total energy ?  thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] a gro file at the end of simulation

Dear All I have done the lysozyme tutorial and at the end of the simulation a .gro file have been produced. would you please tell me whether this gro file contains the structure of our molecules at the end of simulation or not? I mean does it show the simulation box at the end of

[gmx-users] (no subject)

Dear All I have done the lysozyme tutorial and at the end of the simulation a .gro file have been produced. would you please tell me whether this gro file contains the structure of our molecules at the end of simulation or not? I mean does it show the simulation box at the end of

[gmx-users] a problem using g_sgangle

Dear gmx users I am trying to analyze the results of my simulations. a system including one CNT+12 small molecules.I would like to know the distribution of angles formed by  these 12 small molecules around CNT.I have found from manual that g_sgangle may do that however, in the manual has been

[gmx-users] restarting simulation after segmentation fault

Dear gmx users I am simulating a system involving carbon nanotube. I successfully completed the EM,NVT and NPT equilibration phase and then started to run production  simulation(NVT ensemble) for 10 ns.However, after passing more than 50 steps(1 ns),I gave the segmentation error.I

[gmx-users] (no subject)

Dear Justin I really appreciate for your reply. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the

[gmx-users] keep the nanotube cylindrical.

Dear gmx users I am simulation a system including carbon nanotube+water.I have done these things: 1. I copied oplsaa.ff folder in my working directory 2. I added following lines to atomname2type.n2t C    opls_995    0  12.011  2    C  0.142  C 0.142 C    opls_996    0  12.011  3    C 

[gmx-users] how to keep nanotube cylindrical

Dear Justin I appreciate for your reply.I used -maxwarn option because grompp gave me: WARNING 1 [file ffbonded.itp, line 2705]:   Overriding Bond parameters.   old: 0.151 292880 0.151 292880   new: C   C  1   0.1418   478900 I guess I am not using improper in the topology file.my cnt.top file