[gmx-users] Question about MD simulation

bo yang suriayang at gmail.com
Wed May 30 22:05:13 CEST 2007

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 same energy minimization em.mdp file for my nanotube-water
simulation. Since I am using amber forcefield, I changed the name of all
atoms (C, H) of my nanotube according to the name used in ffamberXX.itp.
For example, C is renamed as amberXX_42.
During the energy minimization, I got warning messages as:
WARNING: Writing out atom name (amber) longer than 4 characters to .pdb file
Also, the EM result is "Segmentation Fault".

Can anyone give me some suggstions or hints how to solve the problem?
Is there any other ways to rename those atoms (either in NT or amber files)?

Thank you very much!
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