[gmx-users] Re:

[TJ Piggot]

You should look at the ATP topology and see if the parameters you are using 
look sensible. Where did you get the topology from, did you use the united 
atom one already in the GROMOS96 ff? Also did grompp give you any warnings 
before your minimisation?

Tom

--On Thursday, August 16, 2007 01:04:55 +1000 Mark Abraham 
<Mark.Abraham at anu.edu.au> wrote:

> mjduan at smail.hust.edu.cn wrote:
>> Dear Mark:
>
> Please keep correspondence on the list for others to see and use.
>
>> Thanks for your help about my problem of running GROMACS energy
>> minimization.  I do what you suggestion,  and the protein's minization
>> seems to be correct, it run about 300 steps and the Ep convergent
>> finally, but the ATP's minimization stopped  at 14 stpes. So it means
>> the ATP's topology is broken? what is it means? What should  I do?
>
> So how do you think you would be able to tell whether either or both of
> these chemical structures were in a sensible energy minimum? What
> observables will be useful to you here?
>
> Mark
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.