Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate.
Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v My questions are: 1) Can I get the proper solvent-air interface to obtain density profile by extending the Z direction (last line of the gro file obtained from NPT at each pressure)? Is that what yo mean by " then build a new unit cell and run under NVT" ? 2) Is the semi isotropic option with 0 compressibility in Z is appropriate to keep the pressure fixed? (as shown below in mdp settings)? 3) If the answer to q 2 is negative, whats is appropriate way to shift from NPt to NVT run. Do I have to use the equilibrated density from NPT runs and edit the last line of gro from -c flag of NPT.gro to obtain the correct density? The reason I am asking is that since P fluctuations are huge I am not sure if the the density of box from last frame of -c NPT.gro output is the correct density... Please advise on the above queries..Thanks a lot Below is the md.mdp contents: pbc = xyz integrator = md dt = 0.001 nsteps = 20000000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 100;1 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = Shift vdw-type = Shift rcoulomb-switch = 1 rvdw-switch = 1 ;0.9 ; Cut-offs rlist = 1.35 rcoulomb = 1.1 ;1.1 rvdw = 1.1 Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 425 * * *Pcoupl = berendsen* *Pcoupltype = semiisotropic * *tau_p = 1 0.5 * *compressibility = 3.5e-5 0* *ref_p = 50 ** * gen_vel = no gen_temp = 500.0 gen_seed = 173529 constraints = none constraint-algorithm = lincs On 31 March 2013 12:47, Justin Lemkul <[email protected]> wrote: > > > On 3/31/13 12:27 PM, Elisabeth wrote: > >> Thank Justin. I am interested in the density profile at the solvent-air >> interface. I wanted to see how density changes with position at different >> pressures...I have the equilibrated boxes at several pressures obtained >> from NPT but I am not sure whether running g_density on the current >> simulations cells provides the profile I am after. Do you have any clue >> whether or not the cell has to be extended in one direction to obtain the >> density profile? >> >> > If you're trying to produce an air-water interface, then indeed you will > need some model for air within the unit cell, but there are several > practical problems with that. The first is that g_density does not deal > well with changing box vectors, and the density profiles it produces under > an NPT ensemble are incorrect (outstanding bug that needs to be fixed, > IIRC). The second is that if you run a simulation under NPT with void > space, the unit cell will just compress down until there is no empty space. > Probably the best solution would be to equilibrate under NPT at the > desired conditions, then build a new unit cell and run under NVT. Using > NVT will circumvent both problems, and if the proper pressure, density, etc > have already been achieved, then you've got what you're after. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
