[gmx-users] problem with generating itp file for my own ligand

Hi everyone! I know there are some programs/servers such as PRODRG which can help us to generate the itp files for specific ligand. However, the system now I am working on is Gromacs OPLSAA, I wonder if there are other programs besides PRODRG which can generate the topology/itp files of my

Re: [gmx-users] problem with generating itp file for my own ligand

Lam Yan, Sonia wrote: Hi everyone! I know there are some programs/servers such as PRODRG which can help us to generate the itp files for specific ligand. However, the system now I am working on is Gromacs OPLSAA, I wonder if there are other programs besides PRODRG which can generate the

[gmx-users] image centering

Dear users, I have a membrane simulation trajectory, in which the solvent (water and ions) is separated by lipid bilayer. I want to center the solvent so that the membrane is separated by two layers at the bottom and top in the unit cell. I have tried the followings. trjconv -f ../Eq9/eq9.xtc

[gmx-users] center of mass removal

Dear all, I am simulating short peptide in GROMACS. Center of mass need to be removed to keep the peptide from jumping out. I have two questions about this: 1, when I remove COM of the peptide using comm_grps, do I need to put the solvent(including the counter ion) at the same time for COM

[gmx-users] scalability of gromacs-3.3

Dear all I am trying to scale gromacs on BG/L and I am able to run mdrun on BG/L for 32processors. but when i try to run for 64 or 96, by making the *.tpr file: grompp -np 96 -f run.mdp -p topol.top -c pr.gro -o run.tpr and submitting in BG/L: using the following submission file--- # @

[gmx-users] Dimer simulations using Gromacs

Dear All, I wish to do some simulations using dimer of protein. I have generated .gro file for that. I am able to minimize structure, but when I am trying to give it for equilibration run. I am getting error as: Warning: 1-4 interaction between 5786 and 5791 at distance 5.468 which is larger

Re: [gmx-users] center of mass removal

Li Qiang schrieb: Dear all, Hi Qiang, I am simulating short peptide in GROMACS. Center of mass need to be removed to keep the peptide from jumping out. I guess this is only a visual problem, but read page 18 in the manual. I have two questions about this: 1, when I remove COM of the

Re: [gmx-users] center of mass removal

hi Christian, Thanks for the reply. I have plotted the the rate of center of mass motion and found there are peaks with certain time interval. I think that is not only a visual problem but like fly ice cube problem(not sure). As a comparison, when a large protein is simulated, the rate(velocity)

Re: [gmx-users] scalability of gromacs-3.3

Anupam Nath Jha wrote: Dear all I am trying to scale gromacs on BG/L and I am able to run mdrun on BG/L for 32processors. but when i try to run for 64 or 96, by making the *.tpr file: grompp -np 96 -f run.mdp -p topol.top -c pr.gro -o run.tpr and submitting in BG/L: using the following