[gmx-users] Steered MD

[Mike M]

Take a look at this post:

http://lists.gromacs.org/pipermail/gmx-users/2002-November/003378.html





2012/6/5 Miguel Ángel Mompeán García <mig.mompean at gmail.com>

> You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not
> implemented in GROMACS (hope anyone corrects me if I am wrong)
>
>
>
> 2012/6/4 Mike M <nmr.mike.nmr at gmail.com>
>
>> Dear Gromacs Users,
>>
>> I am trying to study the conformational path from state A to state B with
>> targeted molecular dynamics. These two states are two different structures
>> of a peptide that I have calculated after a series of nmr experiments. I
>> have perform 100ns simulations separately of the two peptides to assess
>> their stabilty over the course of the simulations, but now I wonder how can
>> I direct my system A towards the state named as B. In the manual I have
>> read what it is said in the manual about this topic and the usage of -rb to
>> provide the coordinates of the B state, but I did not find out how to
>> properly set the simulation.
>>
>> Has anyone done this before?
>>
>> Thanks,
>> Mike
>>
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>
>
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