Hi all gromacs users, I am new to GROMACS , please help me
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. In gromacs I want to do Following: 1: A & B temperature coupling 2: C not coupling, Free to increase or decrease temperature from its initial temperature 500K 3: after steady state want to get the final temperature of the part C 4: Calculate Heat flux on each part after 100 ps. I used tau_t =-1 for part C but wandering, is it sufficient to keep tau_t =-1 for avobe work? Thanks for your help 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 Thanks for your help ________________________________ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
