E.Lindahl at chem.rug.nl
Thu Nov 29 11:23:05 CET 2001
The best place for this type of questions is to subscribe & post to the gmx-users
list - you'll probably get a better & faster answer, and once a question has been
solved other users can find it in the archives. I'm cc:ing this one there...
> I'm a french student using Gromacs 2.0, and I've a problem with distance
> restrain between 2 atoms.
> I am in the case I need in my simulation that 2 atoms must stay close to each
> other at a distance of 2 Angstrom, with a strenght equal to a covalent bond...
> Actually, I proceed in this way:
> I modify the .top file before the last RUN (ie after minimisation steps) by
> writing the lines:
> #ifdef DISRES
> ;distance restraint
> [ distance_restraints ]
> ;ai aj type index type' low up1 up2 fac
> 899 1250 1 0 1 0.2 0.21 0.22 1.0
> (where 899 and 1250 are the reference number of my two atoms)
> and in my mdp file, I use the NMR refinment with options :
> My questions are :
> Do I modify any of this? Do I use a disre_Tau <> 0?
The weighting and simple/ensemble options only matter when you have more than
one restraint and want to average, so that's ok.
fc is the force constant - 1000 is default, but if you really want something as
as a bond (that's HARD) you can have a look in the forcefields, e.g. the file
ffgmxbon.tip - the "kb" column in the bondtypes section is the force constants.
The "tau" option turns on running average if it is larger than zero - that is we
calculate the running average of the bond length over tau ps, and then apply the
force depending on the average length.
> With my options, how can fluctuate (in length) the bend at a Temperature of
That is not completely trivial to answer - in principle it can be derived by
mechanics; the fluctuations in energy will be of the order kT where k is
constant and T the temperature, and since the energy of the restraint is
the length deviation should be of the order
This might not be a very good measure in practice, though, since there might be a
of other forces trying to separate your restrained atoms. The best option is
to run a simulation and check the output in the log file!
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