[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 ". Pleas

Re: [gmx-users] Strange trjconv error

On Wed, Dec 11, 2013 at 1:11 AM, rajat desikan wrote: > Dear Justin, > > Thanks for the suggestion. > > Producing a .trr in catdcd still failed because it apparently produces a > trajectory without a timestamp. So, I loaded the .dcd into vmd and saved > the coordinates in a .trr file. This worked

Re: [gmx-users] deformation in cnt

On Wed, Dec 11, 2013 at 3:39 AM, Atila Petrosian wrote: > 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 dim

[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

Re: [gmx-users] deformation in cnt

On Wed, Dec 11, 2013 at 10:05 AM, Atila Petrosian wrote: > 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, 99

[gmx-users] Installing Gromacs 4.6.3 using Cygwin

Hello, I am new to both Cygwin and Gromacs, so I apologize in advance if this error is do to my computing ignorance. I downloaded the gromacs-4.6.3.tar.gz file and tried to follow the 'Quick and Dirty Installation Instructions' to install Gromacs 4.6.3 on my new Windows 8 machine, but encountered

[gmx-users] Regarding relative free energy calculation

Dear all, I am trying to calculate relative free energies of hydration between two similar molecules. I want to do the following things: (1) Totally remove the VDW and Coulomb interactions of few atoms (remove their interaction with all atoms). (2) Transform the Coulomb term (partial charge) of

[gmx-users] g_tcaf issue

Hi all. We are having some problem running g_tcaf here. It keeps yielding "segmentation faults". We first thought it was because of the single-precision calculations of the first run, or the exceedingly large trajectory file. Both were changed for a second trial, which still yielded the same erro

[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 incorrectly.

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 I'm

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 wrote: > On Mon, Dec 9, 2013 at 1:44 AM, Michael Shirts wrote: > >> So, I'm trying to compile with MPI using mpich3. Previous >> installations worke

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 P

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 give

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 -o mut.gro -p topol.top • editconf -f mut.gro