>> Zifeng Li lizife...@gmail.com >> Dear Gromacs users, >> >> I want to compress a polymer slab and solvate it with water to exam the >> interface between them. To prevent the polymer from crossing the interface >> along z direction, I compress it using 2 walls by moving them towards each >> other a little bit ( 0.5 sigma of wall atoms) and equilibrating for 50ps >> subsequently each time. However, the pressure is enormously high during this >> process. >> >> From polymer handbook, this slab should have a density of 0.98g/cm3 at 400K, >> 1bar. >> In my simulation, the density-pressure relation is : >> >> density(g/cm3) Avg. pressure(/bar) >> 0.45 80 >> 0.63 245 >> 0.86 2500 >> >> Gromacs version: 4.5.4 >> >> Here's my NVT.mdp settings: >> >> constraints = none >> integrator = md >> dt = 0.001; 1fs. >> nsteps = 50000; total 50ps. >> ;neighbour searching >> nstlist = 10 >> rlist = 1.1 >> ns_type = grid >> >> ;coulomb >> coulombtype = PME >> rcoulomb = 1.1 >> ewald_geometry = 3dc >> >> ;walls(9-3 type by default) >> pbc = xy >> nwall =2 >> wall_atomtype =opls_139 opls_139 >> wall_density = 50 50 ( set is as 1g/cm3) >> >> ;vdw >> rvdw = 1.1 >> vdwtype = shift >> >> ;output control >> nstxout = 1000 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstenergy = 1000 >> ; Generate velocites is on at 400 K. >> gen_vel = yes >> gen_temp = 400.0 >> gen_seed = 173529 >> >> ;temperature coupling >> tcoupl = v-rescale >> tc-grps = Polymer >> tau_t = 0.1 >> ref_t = 400 >> >> equilibrating the output of compression which has density 1.0 and run a NPT >> with walls, it keeps expanding to density 0.1 g/cm3 after 6ns. >> I doubt this high pressure issues might be caused by wall settings or >> ewald_geometry settings. >> >> 1. For the wall settings >> >> The density of wall (1g/cm3) is close to the density of my system >> (0.45~1g/cm3) and each time I run a NVT, the distance between wall and >> system is 0.5 sigma of wall atoms, the energy between wall and system is 4% >> of the total energy of my system. I don't know what's wrong or what I can >> check next.
any problem with wall settings? > > >>Therefore, I just remove the wall and check the ewald_geometry. >> 2. For ewald_geometry = 3dc >> >> >From the paper J.Chem.Phys.111(1999) pp3155-3162 on Ewald summation for >> >systems with slab geometry, it requires the length of box in z direction >> >should be at least 3 times of that in x/y direction to use this psudeo-2D >> >PME. >> >> However, to simulate such a thick slab would be computationally expensive. >> Therefore, I put vacuum above and below the slab(at slab density 0.45), >> running a NVT without walls(10ns), the pressure goes down to some negative >> value near 0 and the polymer compresses itself in z direction to density >> avg. 0.63 along this NVT and stops shrinking. The density(0.63) is too low >> compared to my expectation(1.0g/cm3). However, I check the density profile >> and find in the middle of the slab, it has bulk density(nearly 1.0g/cm3) and >> the density decrease towards the interface. It seems reasonable since it has >> right bulk density in the middle but I lose control of pressure( along z, it >> is 0 because of vacuum) and density( the avg. density value is low). > > > Is this a correct or efficient way to use 3d ewald correction when you > don't want a thick slab? >> >> >> Thanks! >> >> --Zifeng -- 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