[gmx-users] Generation of the Distance Restraints

[James Starlight]

Justin,

1) I've already tried to examine this graphs but have not understood the
meaning of the Ro value.

E.g I have known distance restrains for the pair of residue wich are 1<r<
2  for instance. As I understood the R1=1 and R2=2 but what about R0 ?As
I've understood  this value might be slightly less than R1 ( e.g 0.9). Does
this correct and how I could specify R0 more accuracy?


2) Besides I want to know if there are possible way to gradyally decrease
force constants during MD run? E.g I want to dicrease this value each 100ps
on the desired value. Is there any way to defind this step value in the MDP
file or should I re-run mu simulation X times started from the previous
short run with bigger forses applied?


James

13 марта 2012 г. 17:19 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

>
>
> James Starlight wrote:
>
>> Mark, Justin,
>>
>> Thanks for advises. Indeed I think that simple text editor would be
>> better sollution in my casw because of small number of restraints.
>>
>> I just have a question about definition of the Distances
>>
>> This is the default of the restraints between atom 10 and 16.
>>
>> [ distance_restraints ]
>> ; ai aj type index type' low up1 up2 fac
>>  10 16 1    0     1     0.0 0.3 0.4 1.0
>>
>>
>>
>> I'd like to restrict distance between both of that atoms   7.96 <
>> r(Ca-Ca)< 8.41
>>
>> I've found that the up1 is the 7.96 and up2 is the 8.41 but how I could
>> specify 'low' in the above table ? Should I obtain value for the initial
>> Ca-Ca distance between my residues from the initial structure? How I could
>> do it?
>>
>>
> See Figure 4.13 and equations 4.79 in the manual.  r0 = low, r1 = up1, and
> r2 = up2.
>
>
> -Justin
>
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> ==============================**==========
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> Justin A. Lemkul
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