Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried productive runs. Now, no matter what I did, it crashed after few ps's of free MD or during the PR runs.
Few of the things I had tried are: 1. Running the simulations on different systems (OSX, linux or blue-gene). 2. Using single or double precision versions. 3. An equilibration stage, 1ns long with a time-step of 1fs, during which the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. 4. Running part of the equilibration stage as NVT and then switched to NPT. 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom. Finally I had moved back to 4.0.7 which worked like charm. I wonder if someone else had encounter something like this. Attached please find the mdp files I used. All the best, Itamar.
pr.mdp
Description: Binary data
md_start.mdp
Description: Binary data
em.mdp
Description: Binary data
----- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu ============================================
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