Re: [gmx-users] Simulation Crash...Reg

Kishore wrote: Dear All, I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in simple spc water in a dodecahedron box. I could easily walk through till the NVT equilibration step after which every thing seems so right(after 5 steps with time step of 2fs using V-rescale t

[gmx-users] Simulation Crash...Reg

Dear All, I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in simple spc water in a dodecahedron box. I could easily walk through till the NVT equilibration step after which every thing seems so right(after 5 steps with time step of 2fs using V-rescale thermostat the system e

[gmx-users] simulation crash with GROMOS96 force field

Dear Vitaly: 1. No problem at all in vacuo? That with a 1 fs timestep and the sd integrator? Strange then that your molecule is ok and the water is ok, but they are unstable together. Perhaps your'e not getting any LJ interactions (or not correct ones) between your solute and water? That's wh

[gmx-users] simulation crash with GROMOS96 force field

All the directives are correct. Chris just mistyped saying [ molecules ] CIP 3 instead of [ moleculetype ] CIP 3 that I orginally send him. Not true. I meant exactly what I typed. I am referring to the section that occurs at the end of your .top file: It sometimes looks like this

[gmx-users] simulation crash with GROMOS96 force field

1. Is your system is properly minimized 2. If you take the output from a 500 ps run with 0.25 fs timestep and start a 1 fs timestep run, is that new run stable? 3. What are atoms 62 and 80? **4. Why is there a 1-4 between atoms 62 and 80 if you have only water and a 42 atom solute? 5. What do

[gmx-users] simulation crash with GROMOS96 force field

Hi all, I am trying to simulate a small organic molecule (42 atoms with 18 hydrogens among them) in water (SPCE). The force field was generated with X2TOP utility using GROMOS96 force field. All bonds, pairs, angles, dihedrals, etc are OK and the system runs OK but sometimes it craches producing s

Re: [gmx-users] simulation crash

[EMAIL PROTECTED] wrote: I use constraints on the c-alpha atoms, so the helix should be stable. I of course optimized the starting geometry, I tried to use the output geometry of a 600 K run as input file, and I tried the simulation with a larger box, but none of this worked. What else can I try