Re: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

Claus Valka wrote: Dear gromacs users, I sent this e-mail as how someone can avoid an error that occured during a simulation. The solution I proposed was just increasing the tables extention parameter in the mdp file. The error concerned the bonded interactions and it had to do with bad equil

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

r her querries. Thank you. Yours Sincerely, Nikos --- Claus Valka schrieb am Mi, 4.3.2009: Von: Claus Valka Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "Discussion list for GROMACS users" Datum: Mittwoch, 4. März 2009, 16:12 H

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

Berk Hess schrieb am Mi, 4.3.2009: Von: Berk Hess Betreff: RE: WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "Discussion list for GROMACS users" Datum: Mittwoch, 4. März 2009, 14:00 --- Berk Hess schrieb am Mi, 4.3.2009: Von: Berk Hess

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

am Mi, 4.3.2009: Von: Berk Hess Betreff: RE: WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "Discussion list for GROMACS users" Datum: Mittwoch, 4. März 2009, 14:00 Hi, The question is not if you are using electrostatics or not, but how large your

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

ct: WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 To: gmx-users@gromacs.org --- Claus Valka schrieb am Mi, 4.3.2009: Von: Claus Valka Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "Berk Hess"

RE: WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

: lastexile...@yahoo.de Subject: WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 To: gmx-users@gromacs.org --- Claus Valka schrieb am Mi, 4.3.2009: Von: Claus Valka Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs

WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

--- Claus Valka schrieb am Mi, 4.3.2009: Von: Claus Valka Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "Berk Hess" Datum: Mittwoch, 4. März 2009, 12:47 Dear Sir Berk, Thank you for your quick response. I simulate a system which has

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

? Berk Date: Wed, 4 Mar 2009 03:12:19 -0800 From: lastexile...@yahoo.de Subject: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 To: gmx-users@gromacs.org Hello, the system I'm referring at is an already equilibrated one. Before, I had already made ste

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

rease it very much and not bother with it. Is there any difference in newest versions? Does it affect anything more? Thank you, Nikos --- Berk Hess schrieb am Mi, 4.3.2009: Von: Berk Hess Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

Hi, Your solution seems to indicate that your system is unstable. My guess is that your system was not well equilibrated and at some point some non-bonded interactions were at a distance of more than cut-off+tab_ext. That would make your system explode. In that case increasing tab_ext to 2 nm