[gmx-users] Energy Minimization

Steven Neumann s.neumann08 at gmail.com
Tue Jan 10 12:13:41 CET 2012

Thank you. Should I also copy and paste coordinates of my ions or just my


On Tue, Jan 10, 2012 at 11:03 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 10/01/2012 9:54 PM, Steven Neumann wrote:
>> Dear Gmx Users,
>> I am setting up my simulations of carbon tube with protein. I solvated my
>> system, added ions and I would like to run EM of my system. My carbons of
>> the tube in MD will be restrained. In this case should I run EM of my
>> protein in water (and with ions) separately and the copy coordinates and
>> then process with NVT and NPT or run EM with restrained nanotubes of my
>> system directly?
> The former is less likely to have problems.
> Mark
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