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 --
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