[gmx-users] how to make a rigid entity

I would like to calculate the PMF between two nanotubes covered with surfactants. for doing this, one nanotube have to hold fixedly and another one have to move as rigid entity. for fixed nanotube I used position restraints, however, I do not know how to make a nanotube a rigid entity? I would be

[gmx-users] how to remove some molecules

Dear gmx-users I would like to calculate the PMF in a system composed of nanotube+surfactants. for doing this I use the final configuration of previous surfactant adsorption simulation onto carbon nanotube. the problem is I want to remove some of non-adsorbed surfactant molecules. Would you

[gmx-users] how to remove some molecules

Thank you Sir for your reply. but I do not know how to recognize the non-adsorbed molecules in a gro file? Is there any way to recognize them in a gro file( I have seen the in VMD)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] (no subject)

Dear gmx users I am analyzing simulation results of a system including carbon nanotube+surfactant molecules. I would like to calculate the number of surfactants located on a specific distance(say 1 nm ) from nanotube in each timestep or average of that quantity.I would be really appreciated if

[gmx-users] calculation of angle between two groups

Dear gmx users I did the simulations of carbon nanotube+surfactant+water molecules and I would like to calculate probability distribution of the angle formed between the vector of the surfactant molecules and CNT. Is there any tools or programs in gromacs to do that?I have tried g_sgangle program

[gmx-users] calculation of angle between two groups

Dear Mark thank you for your concern.when I tried the g_sgangle program it gave me Fatal error: Something wrong with contents of index file. the index file was the one I used during the simulation and I made that with this command: make_ndx -f em.gro -o index.ndx and the groups for temperature

[gmx-users] segmentation fault during equilibration

Dear gmx users, I am simulating a system including carbon nanotube(a finite one)+water+surfactant and so far I have done these things: 1.I generated the topology of CNT ( opls force field) by this command: g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT 2.I used TopolGen to produce

[gmx-users] segmentation fault during equilibration

thank you Sir for your reply.below I provide you .mdp file: title = UNK-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the UNK and LIG ; Run parameters integrator = md; leap-frog integrator nsteps = 5; 2 * 5 = 100 ps dt

[gmx-users] Re: gmx-users Digest, Vol 97, Issue 6

-users@gromacs.org Message-ID: 4f9fda32.6010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/1/12 7:19 AM, niaz poorgholami wrote: Dear gmx users, I am simulating a system including carbon nanotube(a finite one)+water+surfactant and so far I have done these things: 1

[gmx-users] segmentation fault during equilibration

Dear Justin the results of EM was: Steepest Descents converged to Fmax 1000 in 77 steps Potential Energy = -3.6802272e+05 Maximum force = 8.9652832e+02 on atom 1556 Norm of force = 1.1512711e+02 thank you for your concern -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] add nonbonded parameter for interaction between CNT and waters

Dear all I am simulating carbon nanotube in water and I would like to use Lennard-Jones potential For interaction between carbon nanotube and waters with these parameters: σco =3.19˚ A εco =0.392 kJ/mol I know that I should add these parameters manually in ffnonbonded.itp however, I have no Idea

[gmx-users] rigid carbon nanotube

Dear All I would be pleased if anyone could tell me how to kept a carbon nantube rigid throughout the simulations ? thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] grompp error for CNT+surfactant simulation

Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomname2type.n2t Copls_9950

[gmx-users] grompp error for CNT simulation

Dear gmx users, I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done these things: 1. I used packmol to create my PDB file and the used editconf to change PDB to gro file. 2. I copied oplsaa.ff folder in my working directory 3. I added following lines to atomname2type.n2t C