Please keep the discussion on the gmx-users mailing list; I am not a private
tutor. Comments embedded below.
On 6/20/13 8:35 PM, Hari Pandey wrote:
Hi Justin,
Thanks for last help.
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
This value of nstlist is much too large.
ns_type =grid
rlist =0.5
coulombtype =pme
rcoulomb =0.5
vdwtype =cut-off
rvdw =0.5
Unless you are using some custom force field that requires 0.5-nm cutoffs, these
values are incorrect.
pme_order =4
ewald_rtol =1e-5
optimize_fft =yes
DispCorr =no
;Brendsen tempereture coupling is on
Tcoupl = nose-hoover
Nose-Hoover is a poor choice for initial equilibration, especially when
generating velocities.
tau_t =0.001 -1 0.001
Setting tau_t = dt is a bad idea and grompp should have warned you about this.
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
If you're using thermostats, you're not simulating in an NVE ensemble.
;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
You have numerous issues, listed above.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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