[gmx-users] trouble minimizing structure with mdrun

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 4 20:22:58 CET 2010

Hi Jack,

> On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>> Hi Jack,


>> After preparation with (V|NA)MD, did pdb2gmx correctly assign chains,
>> or did it tie chains together? In the latter case it would have issued
>> a number of "Long Bond Warnings". Did anything else odd show up in
>> the output of any of those steps? Did you actually read through it?

Post pdb2gmx/grompp output to help us help you.



Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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