[gmx-users] Problem with Position Restraints (before running SMD)!

[Talal E. AlOtaibi]

Hi guys, When I did my SMD simulation by applying load to a certain group of atoms and fixing certain atoms by modifying the topology file, the points that i have fixed moved from there original position. I don't know what the problem is! Any suggestion!  To make what I was doing clear, I started the equilibrium by creating a box and filling it with water. Then I did the energy minimization. After that I heated up and pressurized the structure. Every thing is good so far. After that, I modified the topology file by adding four points that i want to fix as following:; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
     1 1       1000       1000       1000
1330    1       1000       1000       1000              <---------   my 1st point
1426    1       1000       1000       1000              <---------   my 2nd point
1437    1       1000       1000       1000              <---------    my 3rd point1548 1 1000 1000 1000              <---------    my 4th point
#endifThis only what I did to fix the points. The results have shown that the fixid points moved from their original position.   Here is my topology file: ;
;       File '3gm1a.top' was generated
;       By user: onbekend (0)
;       On host: onbekend
;       At date: Sat Jul  2 14:03:14 2011
;
;       This is a standalone topology file
;
;       It was generated using program:
;       pdb2gmx - VERSION 4.5.3
;
;       Command line was:
;       pdb2gmx -f 3gm1a.pdb -o 3gm1a.gro -p 3gm1a.top
;
;       Force field data was read from:
;       /opt/apps/pgi7_2/mvapich1_1_0_1/gromacs/4.5.3/share/gromacs/top
;
;       Note:
;       This might be a non-standard force field location. When you use this topology, the
;       force field must either be present in the current directory, or the location
;       specified in the GMXLIB path variable or with the 'include' mdp file option.
; ; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp" ; Include chain topologies
#include "3gm1a_Protein_chain_A.itp"
#include "3gm1a_Protein_chain_E.itp"
#include "3gm1a_Protein_chain_F.itp" ; Include water topology
#include "gromos53a6.ff/spc.itp"#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
     1    1       1000       1000       1000
1330    1       1000       1000       1000
1426    1       1000       1000       1000
1437    1       1000       1000       1000
1548    1       1000       1000       1000
#endif ; Include topology for ions
#include "gromos53a6.ff/ions.itp" [ system ]; Name
PROTEIN TYROSINE KINASE 2 BETA; 5 RESIDUES 861-1009; PAXILLIN in water [ molecules ]; Compound        #mols
Protein_chain_A     1
Protein_chain_E     1
Protein_chain_F     1
SOL         8788
NA          25
CL          18
 And Here is my mdp file: title           = smd_120 ; 120 pN
; this is loosely based off of the VT pulling tutorial; heavily modified 
; Run parameters
integrator      = md
dt              = 0.002
tinit           = 0
nsteps          = 2500000       ; 5 ns
; Output parameters
nstxout         = 1000          ; every  2 ps
nstvout         = 1000
nstfout         = 5000
nstxtcout       = 5000          ; every ps
nstenergy       = 1000
; Bond parameters
constraint_algorithm    = lincs
constraints             = hbonds
lincs_iter      = 1              ; accuracy of LINCS
lincs_order     = 4              ; also related to accuracy; Single-range cutoff scheme
nstlist         = 5
ns_type         = grid
rlist           = 1.4
rcoulomb        = 1.4
rvdw            = 1.4
; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.16
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl          = Nose-Hoover
tc_grps         = Protein Non-Protein
tau_t           = 0.2 0.2
ref_t           = 310 310
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 1.0
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocities is off
gen_vel         = no
; Periodic boundary conditions are on in all directions
pbc             = xyz
; Long-range dispersion correction
DispCorr        = EnerPres
; COM motion removal
; These options remove comm motion of the constraint / freeze group
nstcomm         = 1
comm_mode       = Linear
comm_grps       = System
; pull parameters
pull            = constant_force
pull_geometry   = direction
pull_nstxout    = 500 ; will print the c.o.m. coordinates
pull_nstfout    = 500 ; forces on group
pull_ngroups    = 1
pull_group0     = Protein ;
pull_group1     = group_B ;
pull_pbcatom1   = 100 ; the CA of the 10th residue
pull_vec1       = -2.63 -16.48 -14.95 ; direction of pull, will be normalized
pull_k1         = 72.29 ; pull_k1*1.66 = pN;  units: [kJ / (mol * nm^2)]     What should I do?  Thanks,Talal  		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120119/672bd964/attachment.html>