[gmx-users] bypassing pdb2gmx

hi everyone, I have a pdb file of my system and i want it to be fed into the GROMACS software. I have a new force field for the simulation and i have made the .top file manually which includes the new library FF files. I need to get a .gro file from the .pdb file that i have. So, is there a way out

Re: [gmx-users] mdrun running without simulating new steps

st wrote: Hi, I now minimized the energy before the mdrun, and still got the same problem. I also tried several other things: 1. I mdrun the system without water, it runs fine. But once I added water, it stops propagating steps/files while still seems running. 2. The system has nonzero charg

Re: [gmx-users] mdrun running without simulating new steps

Hi, I now minimized the energy before the mdrun, and still got the same problem. I also tried several other things: 1. I mdrun the system without water, it runs fine. But once I added water, it stops propagating steps/files while still seems running. 2. The system has nonzero charge of 0.9, and

[gmx-users] Errors in constraint pulling

Dear GROMACS users, I am trying to calculate the potential of mean force (PMF) of a molecule (A) across phospholipid bilayer (LIP) using constraint method. I am using GROMACS ver 4.0.4. RUN parameters are as follows --- in

[gmx-users] Question about the Marrink's CG model

Dear GMXers: I'm sorry to disturb you. I have a question about the Marrink's coarse-grained model, Marrink, et al. Coarse Grained Model for Semiquantitative Lipid Simulations. J. Phys. Chem. B 2004, 108, 750-760. In the Marrink's CG model, the electrostatic Coulombic potential is computed via

Re: [gmx-users] Keeping PBC during minimization

Francesco Rao wrote: Dear all I have a water box (without any protein or ion). I would like to minimize the box using PBC. My input file looks something like: integrator = steep ; Algorithm (steep = steepest descent minimization) pbc = xyz emtol = 0.1 ; Stop m

[gmx-users] Keeping PBC during minimization

Dear all I have a water box (without any protein or ion). I would like to minimize the box using PBC. My input file looks something like: integrator      = steep         ; Algorithm (steep = steepest descent minimization) pbc = xyz emtol           = 0.1           ; Stop minimization when the maxi

Re: [gmx-users] 1-4 interaction warning

David Wright wrote: Dear GROMACS users, When I started to run a simulation with GROMACS 4.0.4, I got a warning message as following at the beginning and the simulation crashed immediately: Warning: 1-4 interaction between 64 and 73 at distance 15.455 which is larger than the 1-4 table si

[gmx-users] 1-4 interaction warning

Dear GROMACS users,   When I started to run a simulation with GROMACS 4.0.4, I got a warning message as following at the beginning and the simulation crashed immediately: Warning: 1-4 interaction between 64 and 73 at distance 15.455 which is larger than the 1-4 table size 2.400 nm These are