[gmx-users] (no subject)

[Hari Pandey]

Hi all  gromacs users

I have following (NVT.mdp) (NPT.mdp)  and (NVE.mdp)   .  I have three parts of system, A, B and C.
I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B.

What I want is: after some ps,  temperature of A and C should be constant (i.e reach up to steady state) and  B may not be.

for that My NVT.mdp is:
; simulation at 300K and 2 ps is on
        constraints     =all-bonds
        integrator      =md
        dt              =0.001 ; ps
        nsteps          =100000 ; total 100 ps
        nstcomm         =10
        nstxout         =1000
        nstxtcout       =0
       
 nstvout         =0
        nstfout         =0
        nstenergy       =100
        nstlist         =100
        ns_type         =grid
        rlist           =0.5
        coulombtype     =pme
        rcoulomb        =0.5
        vdwtype         =cut-off
       
 rvdw            =0.5
        pme_order       =4
        ewald_rtol      =1e-5
        optimize_fft    =yes
        DispCorr        =no


;Brendsen tempereture coupling is on
        Tcoupl          = nose-hoover
        tau_t           =0.001 
 -1   0.001
        tc-grps         =A  B   C

        ref_t           =750      300       350


;pressure coupling is on
        Pcoupl          =no
        Pcoupltype      =isotropic
        tau_p           =0.5
        compressibility =1e-5
        ref_p           =0.5
;generate velocities at 300 k i.e. at room
 tempereture
        gen_vel         =yes
        gen_temp        =750  300  350
        gen_seed        =-1

MY NPT.mdp is:

( here all output control parameters also)


;Brendsen tempereture coupling is on
        Tcoupl          =nose-hoover
        tau_t           =1  -1   1
        tc-grps        
 =NCALPHA MIDDLE NCNN
        ref_t           =750  300 350



;pressure coupling is on
        Pcoupl          =Berendsen
        Pcoupltype      =isotropic
        tau_p           =0.5
        compressibility =1e-5
        ref_p           =1
;generate velocities at 300 k i.e. at room tempereture
        gen_vel         =no
       
 gen_temp        =750 300 350
        gen_seed        =-1

MY NVE.mdp is:
( here all output control parameters also)
  tc-grps         = A  B  C
       
 ref_t           =750 300 300
        energygrps      = NCALPHA  MIDDLE  NCNN
        tcoupl         = nose-hoover
        tau-t          = 1  -1   1
;pressure coupling is on
        Pcoupl          =no
        ;Pcoupltype      =isotropic
        ;tau_p           =0.5
        ;compressibility =1e-5
       
 ;ref_p           =0.5
;generate velocities at 300 k i.e. at room tempereture
        gen_vel         =no
      ;  gen_temp        =750  300  350
       ; gen_seed        =-1



What I did is:

pdb2gmx - argnew.pdb -o fws.pdb -p  fws.top;
editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0;
grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5;
mdrun -deffnm  em -v;
grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx  -o nvt.tpr -maxwarn 5;
mdrun -deffnm nvt -v;
grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx  -o npt.tpr -maxwarn 5;
mdrun -deffnm npt -v
grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx  -o nve.tpr -maxwarn 5;
mdrun -deffnm nve -v;

g_energy -f nve.edr -s nve.tpr -o F1.xvg



But the system do not get equilibrated and A, B has not steady state temperature  after   time
 even 100 ps. please help me, where I did wrong


Thanks for your help




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