[gmx-users] How to run multiple (different) distance restrains in the same simulation?

[Justin Lemkul]

On 9/2/19 2:14 PM, Tanos Franca wrote:
> Dear users,
>
>       I´m trying to run a MD simulation using different distance restraints
> for several pairs of atoms in a large ligand (example: 0.1 nm - 0.2 nm; 0.2
> nm
> - 0.3 nm, ...) but it´s not working. GROMACS is only accepting one range of
> restraint (example: 0.1 nm - 0.2 nm for all pairs) per simulation. If
> I try including different ranges I get the fatal error message bellow.
>       I'm doing it according to item 4.3.5 of GROMACS manual and including
> the distance restrains in the .itp file of the ligand as described below.
>      Does someone knows how to run the different range of distances in the
> same MD simulation?
>       Bests,
>       Tanos França.
>
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1.4
> Source code file:
> /home/cuda1/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/readir.c,
> line: 3872
>
> Fatal error:
> Found 2 double distance restraint indices,
> probably the parameters for multiple pairs in one restraint are not
> identical
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> [ distance_restraints ]
> ; ai       aj     type     index     type'     low     up1     up2     fac
>    54      33        1         0         1     1.8     1.8     2.5     1.0
>    64      63        1         0         1     2.5     2.5     3.5     1.0
>    25      65        1         0         1     2.5     2.5     3.5     1.0
>    34      42        1         0         1     2.5     2.5     3.5     1.0
>    63      14        1         0         1     2.5     2.5     3.5     1.0
>    53      25        1         0         1     3.5     3.5     4.5     1.0
>    14      62        1         0         1     3.5     3.5     4.5     1.0
>    14      13        1         0         1     3.5     3.5     4.5     1.0
>    54      34        1         0         1     3.5     3.5     4.5     1.0

Assign each to different indices. The index specifies to which signal 
the restraint corresponds (as in NOE), so there can only be one set of 
parameters for index.

-Justin

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Justin A. Lemkul, Ph.D.
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