[gmx-users] Elastic network model

[Warren Gallin]

GROMACS uses nm as the unit of length, so this is 38 Angstroms, shouldn't be a problem.


On 2012-08-31, at 2:23 PM, Bogdan Costescu <bcostescu at gmail.com> wrote:

> On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena
> <maruthi.sena at gmail.com> wrote:
>> Hi all,
>>             I have built topology for elastic network as follows(the
>> atoms which fall with in a distance less than 6 angtroms are bonded).
>> [bonds]
>> ;ai    aj   funct               bo     kb
>> 2       1       1       3.80444752888   61.9
> 
> Less than 6 Angstrom ??? You need to read the topology chapter of the
> manual again. And then again. It will save you lots of time later.
> Hint: some units are wrong.
> 
> Good luck!
> Bogdan
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