Thank you Mark for your answer! I agree with you when you say that the high pressure is not itself a problem. To avoid that problem I change my system from 1000 molecules to 27000 molecules, and the pressure change from several thousands to several hundreds bar. What I found very strange was the increasing volume (and pressure). My system is very unstable, I know, because the density is very low, and not the opposite, so I was expecting to see the box getting smaller. Looking to the trajectory I can see a box almost empty (with empty I mean empty space, with chloroform molecules aggregating in small droplets), and that's why I found the system behavior very strange.
I will follow your suggestion concerning nsttcouple and nstpcouple and the other initial conditions. Nuno Azoia On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham <[email protected]> wrote: > On 12/10/2011 2:22 AM, Nuno Azoia wrote: >> >> 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. > > The high pressure is not itself a problem - small numbers of molecules and > short simulation times lead to doubtful statistics for pressure. > >> Then I change to >> NPT conditions and both the pressure and the volume keep increasing >> with time. > > Be sure to visualize your trajectory to confirm its behaviour matches what > you expect from the trends in P and V. > >> >> 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? > > It seems you are generating some numerical instability with your choice of > initial and simulation conditions, and that gromacs-4.0 was luckier in > avoiding the problem. If this is a parallel simulation, then the way > communication is managed in order to organize T and P coupling changed going > up to 4.5. For equilibration, I would encourage setting nsttcouple and > nstpcouple to 1. Using a shorter time step can help with numerical > instability. Berendsen T coupling or a larger coupling time constant might > also help. After gentler NVT, then switch to NPT, let the box size > stabilize, and finally move to larger coupling periods, time steps and > v-rescale T coupling. > > Mark > >> >> >> 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 >> > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Nuno Gonçalo Azoia Lopes Rua Nascente, nº 25 4705-473 Escudeiros Tel: 253 683 198 Móvel: 965 382 487 -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
