[gmx-users] deformation in cnt

Dear Justin Thanks for your reply. After energy minimization, all carbon atoms are in true position, inside box but again, both ends of cnt were deformed, same problem I had before I add bond length to the length of CNT in z dimension of box. You mentioned possibly poor input geometry . Please

Re: [gmx-users] deformation in cnt

On Wed, Dec 11, 2013 at 3:39 AM, Atila Petrosian atila.petros...@gmail.comwrote: Dear Justin Thanks for your reply. After energy minimization, all carbon atoms are in true position, inside box but again, both ends of cnt were deformed, same problem I had before I add bond length to the

[gmx-users] deformation in cnt

Dear Justin I built CNT by nano tube modeller. Then, I put protein (fragment model with 15 residues) in appropriate distance of CNT manually. I used force field parameters from following paper: J. Phys. Chem. B 2001, 105, 9980-9987. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] editconf and conect option

Hello I am trying to have gromacs (using editconf) write a connect section to my pdb file, but it keeps failing giving me a strange error about using an old gromacs version 2 when making my pdb file. This is erroneous. I don't even have that version..I'm sure I'm using the command line

Re: [gmx-users] editconf and conect option

On 2013-12-11 20:46, Steve wrote: Hello I am trying to have gromacs (using editconf) write a connect section to my pdb file, but it keeps failing giving me a strange error about using an old gromacs version 2 when making my pdb file. This is erroneous. I don't even have that version..I'm sure

Re: [gmx-users] Compilation issue with F77_FUNC functions?

And looks like the solution was to make sure that mpic++ was used as the compiler instead of mpicc. On Mon, Dec 9, 2013 at 5:22 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Dec 9, 2013 at 1:44 AM, Michael Shirts mrshi...@gmail.com wrote: So, I'm trying to compile with MPI using

Re: [gmx-users] pressure based replica exchange

Thanks very much. As you suggested, making T with small increments such as 300.0, 300.0001, 300.0002 ... leads to complaints :-) I am trying to do replica exchange at different surface tensions for my membrane system. To achieve different surface tensions for different replica, I only changed

Re: [gmx-users] pressure based replica exchange

Pressure replica exchange is not in currently. It will be added eventually (it's not that hard, just takes time, and hasn't been a priority.). Note that pressure temperature control with berendsen pressure control will be 100% wrong. For pressure replica exchange to work, the barostat has to

Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

Hello Everyone， I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but find little useful. My Gromacs was installed in a Linux cluster. Follows is my steps to do normal mode analysis: • pdb2gmx -ignh -ff forcefield -f protein.pdb -o mut.gro -p topol.top • editconf