On 14/03/2012 12:38 AM, James Starlight wrote:
Justin,
1) I've already tried to examine this graphs but have not understood
the meaning of the Ro value.
How about reading the equation on the previous page?
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?
Anything else you've known and understood about distance restraints in
some unknown context doesn't matter. What's written in the GROMACS
manual matters for using them in GROMACS :-)
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?
I already answered this.
http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html
Mark
James
13 ????? 2012 ?. 17:19 ???????????? Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> ???????:
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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