Re: [gmx-users] same simulation, different results

? Thank you, Jim Fonseca On May 16, 2007, at 9:40 AM, Jim Fonseca wrote: Thanks a lot--that was it. On May 15, 2007, at 12:42 PM, David van der Spoel wrote: Jim Fonseca wrote: Hi, Does anyone know what would cause a simulation to change if I run it a second time? I'm starting with

Re: [gmx-users] same simulation, different results

Thanks a lot--that was it. On May 15, 2007, at 12:42 PM, David van der Spoel wrote: Jim Fonseca wrote: Hi, Does anyone know what would cause a simulation to change if I run it a second time? I'm starting with an EM structure and just doing a quick 10 ps simulation. I've foun

[gmx-users] same simulation, different results

help me with this? Thank you, Jim Fonseca title= PG_Ca_ext cpp = /usr/bin/cpp include = -I../top constraints = all-bonds integrator = md tinit= 0.0 dt = 0.002 nsteps

Re: [gmx-users] Which POPC Bilayer to start?

I've had success with Tieleman's lipids.  I used popc128b.pdb. Since it has the extra ns of equilibration, I figured it would cause fewer problems.  However, once you start messing around with making hole in the membrane and adding a protein, you'll need to re-equilibrate again (EM & PR).JimOn Sep

[gmx-users] mdrun segmentation fault

n before running for so long. Thanks for any help! Jim Fonseca *log from parallel node 0* Step Time Lambda 12 240.00.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.067432 7188 7189

Re: [gmx-users] POPC simulation

4. Re: Position restrain (Xavier Periole) 5. Stange results of bonds fep (Oleg Stroganov) 6. POPC simulation (Arindam Ganguly) 7. Re: Simulating crystalls (Yang Ye) 8. Re: POPC simulation (Jim Fonseca) - - Message: 1

Re: [gmx-users] POPC simulation

Arindam, I fixed this problem a while ago and it was pretty difficult to figure out. I tinkered with so many things, once I got it to work I didn't even know what steps I took to fix it! Here's something to try: GROMACS doesn't like the fact popc.itp has a four-character residue name (si

Re: [gmx-users] distance restraints problem

I believe that there's no problem with the numbering.  The numbering in the topology will start with 1, however due to Gromacs' implementation, the indexing starts at 0. So, atom 4036 in your .itp corresponds to 4035 in the trajectory file.  Note that if you look in your trajectory file you should