Hello! I found something very strange while making a CHCl3 box using gromacs-4.5.5. A look the mailing list, the manual and some release notes for gromacs-4.5 and I couldn't found the answer for my problem. It's possible that I'm doing something wrong, but I can not find what, so I'm describe my problem.
I start a chloroform box from scratch, using genconf, and I get o chloroform box with 1000 molecules. I get energy minimization without problems. Then I've run some equilibration steps in a NVT ensemble and in the end I get pressure in the order of hundreds of bar. Then I change to NPT conditions and both the pressure and the volume keep increasing with time. To discard the possibility of a size problem, I repeat everything with a box of 27000 molecules, with a volume of ~13800 nm^3. The problem was the same. Very high pressures (150-200 bar) and very low densities (< 200 g/L) after 750 ps simulation time. And both volume and pressure increasing with time. I'm doing now the same procedure, but using gromacs-4.0.7 and I'm getting very different (and better) results. After energy minimization I run 50000 steps in a nvt ensemble and I got pressure around -30 bar (Ok for me). After that I start to run the simulations in npt ensemble and the pressure start to increase slowly, with negative values because the system have very low densities (~400 g/L), and the volume is decreasing. So I'm getting the normal reaction from the system. Where is the problem? There are some different parameters to set in the mdp file and I didn't realize that, or is this a problem in gromacs-4.5? In both cases I used this parameters: ------------------------------------------------------------------------- integrator = md dt = 0.002 nsteps = 50000 nstcomm = 1 nstxtcout = 500 xtc-precision = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 5 ns_type = grid ;Reaction field rlist = 0.8 coulombtype = Reaction-field rcoulomb = 1.4 epsilon_r = 1.0 epsilon_rf = 4.8 vdwtype = cut-off rvdw = 1.4 ; temperature coupling Tcoupl = v-rescale tc-grps = CHCL3 tau_t = 0.05 ld_seed = -1 ref_t = 300 ; Energy monitoring energygrps = CHCl3 ; Isotropic pressure Pcoupl = no Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300 gen_seed = -1 constraint_algorithm=lincs lincs_order = 4 lincs-warnangle = 90 constraints = all-bonds ------------------------------------------------------------------------ and of course, for the npt ensemble I just change _________________________________________ Pcouple = berendsen gen_vel = no ------------------------------------------------------------------------ Thank you in advance -- Nuno Gonçalo Azoia Lopes -- 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