Dear Gromacs users,<br>
Perhaps it is a simple question, but it will help me a
lot. Is it possible with GROMACS forcefield to simulate in a box
elements without solvent?? Or is the solvent an essential bondary
condition?<br>
Well I could define a box with editconf and run
simulations without using genbox, in a system in which I froze some
molecules and would like to have the protein not frozen. However when
running grompp I got the message "Number of degrees of freedom in
T-Coupling group Protein is 0.00" and "Number of degrees of freedom in
T-Coupling group OHH is 0.00" , and probably as result of it the
temperature was always zero.<br>
Below comes <span style="font-weight: bold;">part</span>
of my .mdp file. I can not see why it occurs (temperature = zero), once
I believe that I applied the frozen group option only for sol, not for
protein. Can anybody help me? Sorry for the long e-mail and thank you
in advance for your colaboration,<br>
Fernando Mattio<br>
<br>
;group(s) to write to xtc trajectory<br>
xtc_grps = protein OHH <br>
;group(s) to write to energy file <br>
energygrps = protein OHHl <br>
;Frequency to update the neighbor list (and the long-range forces, <br>
;when using twin-range cut-off's). <br>
nstlist = 10<br>
;Make a grid in the box and only check atoms in neighboring grid cells <br>
;when constructing a new neighbor list every nstlist steps. <br>
ns_type = grid<br>
;cut-off distance for the short-range neighbor list<br>
rlist = 0.8<br>
;treatment of electrostatic interactions<br>
coulombtype = cut-off<br>
rcoulomb = 1.4<br>
;treatment of van der waals interactions<br>
rvdw = 1.4<br>
; Periodic boudary conditions in all the directions <br>
pbc
= xyz<br>
;Temperature coupling<br>
tcoupl = berendsen<br>
tc-grps = protein OHH <br>
tau_t = 0.1 0.1 <br>
ref_t = 263 263 <br>
;Pressure coupling<br>
Pcoupl = berendsen<br>
Pcoupltype = isotropic<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
;Velocity generation<br>
gen_vel = yes <br>
gen_temp = 263<br>
gen_seed = 173529<br>
;Constrain all bonds<br>
constraints = all-bonds<br>
<br>
freezegrps = OHH<br>
freezedim = Y Y Y<br>