On 8/12/14, 1:57 PM, Nikolaos Michelarakis wrote:
Thank you very much for your answer!
this is the link to the whole forcefield directory:
https://drive.google.com/folderview?id=0Bxa-J2wEpEeqbnZDVmpmQ0JGcUE&usp=sharing
Since it's my first time doing something like that, i might have done
som
On 8/12/14, 12:20 PM, Nikolaos Michelarakis wrote:
An output coordinate file is always produced unless mdrun completely fails
and
seg faults. That doesn't mean the coordinates are sane. It's meant to
help you
diagnose in cases like this where you have an absurd force on some atom.
What
>An output coordinate file is always produced unless mdrun completely fails
and
>seg faults. That doesn't mean the coordinates are sane. It's meant to
help you
>diagnose in cases like this where you have an absurd force on some atom.
>What is atom 2832? What's around it? Is there anything obvi
On 8/12/14, 11:19 AM, Nikolaos Michelarakis wrote:
Hello again,
I finally managed to introduce the iron into my structure and generate a
topology. However, when i first run the initial energy minimization, either
in vacuum or with solvent, i get the following message:
It stopped because the a
Hello again,
I finally managed to introduce the iron into my structure and generate a
topology. However, when i first run the initial energy minimization, either
in vacuum or with solvent, i get the following message:
It stopped because the algorithm tried to make a new step whose size was too
sm
