[gmx-users] gromacs bond restraints

Mark Abraham mark.j.abraham at gmail.com
Fri Jan 17 15:11:26 CET 2014


Hi,

REMD just runs your topology at that temperature and you get whatever the
result is. There is no need for the ensembles to be physical (e.g. NVT at
350K already has an unphysical pressure, and none of the force fields were
parameterized to work over a range of temperatures), they just need to have
an energy distribution that has relevant overlap.

What is it about your model that permits proline to sample unphysical
conformations with energies comparable to phyiscal ones?

Mark


On Fri, Jan 17, 2014 at 7:43 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:

> Hi Mark,
>
> I came across your tutorial on REMD on gromacs website. In the tutorial,
> you don't mention about dihedral or any other restraints during REMD. Sorry
> for my ignorance, but I am trying to figure out if restraints are required
> for residues such as prolines to stop going to cis during REMD above 350K
> or there is any setting which will be take care of it?
>
> Many thanks,
> Neha
>
>
>
>
>
>
> On 16 January 2014 14:59, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
>> See chapter four for what is available, and tables in 5.5 for a summary of
>> their use.
>>
>> Mark
>> On Jan 16, 2014 5:11 AM, "Neha Gandhi" <n.gandhiau at gmail.com> wrote:
>>
>> > How can I impose restraints in gromacs .mdp file or topology file to
>> > avoid isomerization of the peptide bond at the highest temperatures?
>> >
>> > Your help is appreciated
>> >
>> > --
>> > Regards,
>> > Dr. Neha S. Gandhi,
>> > Curtin Research Fellow,
>> > School of Biomedical Sciences,
>> > Curtin University,
>> > Perth GPO U1987
>> > Australia
>> > LinkedIn
>> > Research Gate
>> > --
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>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
>


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