[gmx-users] Question about ffamber in Gromacs

Dear gromacs user, I am doing the MD simulation of CNT-DNA interaction. Before introducing DNA, I used gromacs default force field and finished the simulation of CNT (carbon nanotube). And, in the ffgmxnb.itp, I introduced the non-bonded parameters for C-C and C-OW (oxygen) in the [non-bonded

[gmx-users] Question about CNT simulation

Dear gromacs user, I am doing a CNT-water simulation with using ffamber99 forcefield. I don't know what carbon and hydron atom models I should use. In ffamber99.atp, there are a lot of different C atoms with same mass. Can you give me some suggestion? Cheers! Bo

[gmx-users] about CNT simulation

Dear gromacs users, Thank you for your answering my previous questions. Here, I am in trouble again. I continue the simulation of DNA, carbon nanatube and water. I changed the names of atoms in cnt.pdb according to the names in ffamberXX.itp. When I performed the energy minimization, the result

[gmx-users] Question about MD simulation

Dear gromacs users, I have a quetion regarding using amber forcefield in gromacs. I did the DNA and water interaction simulation. After the energy minimization, the original helix-structured DNA becomes two fragments. At this stage, I assume that the simulation process is correct. I used exactly

[gmx-users] Question about DNA simulation

Hi, When I do the DNA MD simulation. I use pdb2gmx, and the water model I used is spc.gro. I did the editconf and genbox. The following is my em.mdp file. define =-DEFLEXIBLE integrator

[gmx-users] Question about DNA simulation

Hi everyone, I am still lost. For the DNA simulation that I am doing, I really don't know what is wrong. Is the em.mdp file (maybe temperature or other settings) inappropriate? Can you give me more specified explanation? Regards! Bo ___ gmx-users

[gmx-users] Question about DNA simulation

Hi, As I mentioned in my last message, I also use pymol to visualize the molecule with water. I realize that the very top part of the DNA molecule is not surrounded by water molecules. I tried to varying the value for -d. Do you have any suggestions? Cheers~ Bo

[gmx-users] Question about DNA simulation

Hello, I have a question regarding DNA simulation. I have the amber99 package. Can anyone give me an explanation why all the masses in the ffamberXXnb.itpare 0? Thank you very much! Bo ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Problems with forcefield amber99 in Gromacs

Hi, I have a question regarding to using forcefield amber99 in Gromacs. I have all the parameter files of amber99. I am doing the MD of carbon nanotube with DNA. I have changed the .pdb file of the DNA according to the instruction. I generated the topology of DNA with identifying -water