[gmx-users] Distance restraints does not work?

[Christopher Neale]

use mdp option disre=simple
Your output should contain a NOTE telling you this: http://redmine.gromacs.org/issues/265


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Emma Ahlstrand <emma.ahlstrand at lnu.se>
Sent: 12 December 2013 08:22
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Distance restraints does not work?

Hi,
I am trying to do a simulation with distance restraints for the Zn-His(NE2)atoms in a peptide, but the distances are not kept to what I want them to be. Why?

I have added this in my topology.top:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#ifdef ZN
[ distance_restraints ]
355    333      1       1       1       0.1985  0.2231  0.4     1
355    316      1       2       1       0.1985  0.2231  0.4     1
355    156      1       3       1       0.1985  0.2231  0.4     1
355    139      1       4       1       0.1985  0.2231  0.4     1
#endif

And I use the following setting in pr.mdp:
define              =  -DZN
; NMR refinement stuff
disre           = Simple        ; Distance restraints type: No, Simple or Ensemble
disre-weighting = Equal         ; Force weighting of pairs in one dist rest: Equal or Conservative
disre-mixed     = no            ; Use sqrt of the time averaged times the instantaneous violation
disre-fc        = 1000
disre-tau       = 0
nstdisreout     = 100           ; Output frequency for pair distances to energy file

When I look at the structure, two of the restrained His(atom 139 and 333) has left the Zn(atom 355). Some values from the distance analysis are printed below:
g_dist -f traj.trr -s b4pr.tpr -n index.ndx -o dist139.xvg
less dist139.xvg
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@ s0 legend "|d|"
   0.0000000    0.2119962
  24.0000000    0.2470244
  50.0000000    0.4642269
 100.0000000    0.4505744

less dist333.xvg
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@ s0 legend "|d|"
    0.0000000    0.2172887
    24.0000000    0.2171661
    50.0000000    0.4632832
 100.0000000    0.3777701

Why does the distance increase? Why is it not held in between roughly  0.1985  0.2231?

Thanks in advance,
------------------------------
Emma Ahlstrand
PhD student

Linnaeus University
Faculty of Health and Life Sciences
391 82 Kalmar / 351 95 Växjö

+46 480 446 152 Telephone
+46 73 905 7186 Mobile
emma.ahlstrand at lnu.se
http://lnu.se/ccbg
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