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[lammps-users] Reg_Fix SMD
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[lammps-users] Reg_Fix SMD

From: santhosh mathesan <>
Date: Thu, 18 Dec 2014 23:30:49 +0530

Hi all,

I am trying to pull the polymer chain away from the fixed surface. I am using "fix smd" to pull the polymer chain along  z direction.  If am not wrong, I should use either nvt or npt in order to have updated position.  In this case I have the surface fixed using "fix setforce" and one end of chain is fixed using "fix spring/self".

I am not sure which ensemble to use either nvt or npt..  Is there any specific conditions or applications under which these has to be used?

Also, is it possible to apply these ensembles only to the polymer chains, because the position of atoms in surface is not going to change over simulation.

If I use nvt ensemble for the entire system, after some run, the temperature is increasing drastically and I get an error "bond atom missing".

If I use nvt ensemble (300K) for the polymer chain alone  the temperature fluctuation is so high.. It is between 70 to 600 K.

    units real
    atom_style full
    bond_style      harmonic
    angle_style      charmm
    dihedral_style charmm
    pair_style  lj/cut/coul/long 10.5 10.5
    kspace_style     pppm 1.0e-4
    neigh_modify every 1 delay 0 check yes one 10000

Here is my input script.

group HAP id > 2206
group CS id < 2206
group fixed id <> 2002 2206
group end id <> 1103 1127

dump 2 all dcd 10 dump_for_equi.dcd
compute 1 CS temp
fix 1 HAP setforce 0 0 0
fix 2 fixed spring/self 10
fix 3 CS nvt temp 300 300 1
fix 4 end smd cvel 7 -10 tether NULL NULL 150 0
thermo_style custom step temp press vol c_1 
thermo 10
timestep 1
run 10000
unfix 1
unfix 3
unfix 4

Thank you, 
Santhosh. M