[gmx-users] Generation of the Distance Restraints
jmsstarlight at gmail.com
Tue Mar 13 14:38:28 CET 2012
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?
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 A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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