[gmx-users] distance restraints

[Justin A. Lemkul]

On 5/17/12 2:51 AM, Banafsheh Mehrazma wrote:
> Dear all
> I 'd like to do NOE distance restraints;  according to the chapter 4 of the manual;
> I should specify a section for [ distance_restraints] :
>
> [ distance_restraints ]
> ; ai  aj  type  index  type’  low  up1  up2  fac
> 10   16    1    0    1    0.0    0.3    0.4    1.0
> 10   28    1    1    1    0.0    0.3    0.4    1.0
> 10   46    1    1    1    0.0    0.3    0.4    1.0
> 16   22    1    2    1    0.0    0.3    0.4    2.5
> 16   34    1    3    1    0.0    0.5    0.6    1.0
> .................................................................
> althought I've studied the manual, it is still unclear to me, that how is the
> index column defined? what are the numbers (0,1,2,3) implying? what about the
> low, up1,up2, fac columns?
>

All of this information is in the manual, section 4.3.4, under the heading 
"Using distance restraints."

With respect to indices:

"The type column should always be 1. As explained in sec. 4.3.4, multiple 
distances can contribute to a single NOE signal. In the topology this can be set 
using the index column. In our example, the restraints 10-28 and 10-46 both have 
index 1, therefore they are treated simultaneously."

With respect to low, up1, and up2:

"The columns low, up1, and up2 hold the values of r0, r1, and r2 from eqn. 4.77."

For fac:

"In some cases it can be useful to have different force constants for some 
restraints; this is controlled by the column fac. The force constant in the 
parameter file is multiplied by the value in the column fac for each restraint."

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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