1
$\begingroup$

I am trying to separate two methyl-N,N'-diacetylchitobiose sugars using steered molecular dynamics in AMBER. I have tested out:

&rst
iat=-1,-1,
r2=2.5,
rk2=10.0,
r2a=12.5,
iresid=0,
fxyz=1,1,1,
outxyz=1,
igr1=2,5,6,8,9,11,14,16,18,20,22,24,26,27,28,32,33,35,36,38,41,43,45,47,49,51,53,54,55,59,60,
igr2=65,68,69,71,72,74,77,79,81,83,85,87,89,90,91,95,96,98,99,101,104,106,108,110,112,114,116,117,118,122,123
/

Which should apparently separate the two sugars relative to their heavy atoms from a distance (between each other) of 2.5 A to 12.5 A along the x,y and z axes and using a force constant of 10 (I think kcal/mol). The solvent I am using is water.

I ran this separation for 100 ns and the two sugars refused to separate. I am not sure if my force constant is too small, or if something else is wrong with my reference file. I have googled it and spoken to m supervisor about it, and unfortunately I have not succeeded in finding a solution.

Any help would be appreciated.

$\endgroup$
  • 1
    $\begingroup$ Are you sure you have specified the correct groups/residue IDs/atom numbers? If yes, then have you tried increasing the force constant to a very high value, to see whether or not the molecules separate? $\endgroup$ – Bdrs Jun 6 '18 at 8:53
  • 1
    $\begingroup$ The force constant was too low. I managed to fix it now. $\endgroup$ – LLCJ27 Jun 6 '18 at 10:32
0
$\begingroup$

I have realized the problem. The force constant was too low. Increasing it to 25.0 from 10.0 sorted things out.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.