[gmx-users] about md simulation

[TJ Piggot]

Also see

http://wiki.gromacs.org/index.php/Thermostats

As you do not want to temperature couple the sodium ions independently

Tom

--On Tuesday, September 11, 2007 18:14:43 +1000 Mark Abraham 
<Mark.Abraham at anu.edu.au> wrote:

> amri ta wrote:
>> Dear colleagues,
>>
>> I am simulating a phosphorylated protein embedded in waterbox.
>> When I try running mdrun, I get a LINCS warning.
>>
>> Does this mean that I have go back to the CG-EM step and use the double
>> precision libs?
>
> These should help.
>
> http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
> http://wiki.gromacs.org/index.php/blowing_up
> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
>
> Mark
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.