Re: [gmx-users] Help with interpreting message for fatal error

Hi Justin, Thanks again for the tip. I'm always assuming that there's something wrong with my setup but I tested using one rank only and then I get an order of magnitude smaller fluctuations... #underInvestigation -- Viveca On Mon, Mar 12, 2018 at 6:42 PM, Justin Lemkul

Re: [gmx-users] Help with interpreting message for fatal error

Hi Gregory, It's periodically connected and I am applying adaptive biasing/pulling (forgot to say). If you have special experience with that kind of setup, I'd be interested in hearing it. Otherwise, it's quite standard, and yes, parmbsc1. -- Viveca On Mon, Mar 12, 2018 at 6:53 PM, Gregory

Re: [gmx-users] Help with interpreting message for fatal error

On 3/12/18 1:40 PM, Viveca Lindahl wrote: Hi Justin, I'm using semi-isotropic pressure coupling and the periodicity is along z. I should say that I'm also adaptively biasing a base pair to open, which is triggering the fluctuations. I guess you mean using only OpenMP? I have not tried that

Re: [gmx-users] Help with interpreting message for fatal error

Hi Justin, I'm using semi-isotropic pressure coupling and the periodicity is along z. I should say that I'm also adaptively biasing a base pair to open, which is triggering the fluctuations. I guess you mean using only OpenMP? I have not tried that no, thanks for the suggestion. Now I changed to

Re: [gmx-users] Help with interpreting message for fatal error

Hi Viveca, Could you share more details of your simulations that may shed any light?  I assume that you are using parmbsc1 as the DNA forcefield.  Is it an "unusual" system?  We (and I am sure others) simulate DNA (± ligand) quite a bit and would be as interested in understanding what is

Re: [gmx-users] Help with interpreting message for fatal error

On 3/12/18 10:42 AM, Viveca Lindahl wrote: Hi Gregory, In the sense that I see it happening repeatedly yes :) But I can't reproduce it very predictably. After seeing that (for my small system) I get very large box vector fluctuations using Parrinello-Rahman, my current assumption is that

Re: [gmx-users] Help with interpreting message for fatal error

Hi Gregory, In the sense that I see it happening repeatedly yes :) But I can't reproduce it very predictably. After seeing that (for my small system) I get very large box vector fluctuations using Parrinello-Rahman, my current assumption is that there are some stability assumptions made by mdrun

Re: [gmx-users] Help with interpreting message for fatal error

Since there hasn't been any response to your question yet, may I ask: is it reproducible? Gregory On 3/11/2018 7:30 AM, Viveca Lindahl wrote: Hi, I'm running a simulation of a periodic DNA molecule. After some time I get, sometimes the following error message: --- A list of

[gmx-users] Help with interpreting message for fatal error

Hi, I'm running a simulation of a periodic DNA molecule. After some time I get, sometimes the following error message: --- A list of missing interactions: Proper Dih. of 3917 missing 1 Molecule type 'DNA_chain_A' the first 10 missing interactions, except for