[gmx-users] Position restraint problem

Arpita Aravind arpita_aravind at yahoo.com
Wed Nov 27 19:45:08 CET 2002

I am trying to perform MD simulation on my protein
consisting of chains A (451 residues) and B (444
residues) and neutralized by 46 NA+ ions. On
performing "gmxcheck" on the the trajectory file
obtained after the short MD with position restraint, I
find that a large no. of heavy atoms like the carbon
atoms are overlapping (i.e. the average distance
between them is less than the sum of both Van der
Waals radii). 

Inspite of increasing the restraint force in
posres.itp file to 10000 kJ/mol/nm, the carbon atoms
are still overlapping. 

This problem is observed with both the GROMOS-96
forcefield as well as with the OPLS-AA forcefield. 

I tried position restraint on the protein miniminized
using another script (outside GROMACS) and still face
the problem of the carbon atoms overlapping on
performing "gmxcheck".

I am attaching my pr.mdp file below:
title               =  Protein
cpp                 =  /lib/cpp
include	            = -I../top
define              = -DPOSRES
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  10000    ; total 20ps
nstcomm             =  1
nstxout             =  1000
nstvout             =  1000
nstlog              =  1000
nstenergy           =  250
nstxtcout           =  250
xtc_grps            =  Protein 
energygrps          =  Protein SOL NA+
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps             =  Protein  SOL   NA+  
tau_t               =  0.1	0.1   0.1
ref_t               =  50	50    50
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  1.0
compressibility     =  4.5e-5
; Generate velocites is on at 50 K.
gen_vel             =  no
gen_temp            =  50.0
gen_seed            =  173529
constraints         =  all-bonds

Could you please help me and let me know what I am
doing wrong.
Thank you.
With regards,
P.S. Could you please cc the e-mail to:
arpita_aravind at yahoo.com as well. Thank you.

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