Hello Chris, thanks for the tips, they were very helpful. Now a new problem appeared. I'm trying to separate the two benzene molecules from one another while maintaining the displacement vector aligned with the z axis. For that I have used "pull_geometry = direction". However, at the end of the simulation, I notice that the desired alignment (with z) was not maintained. The molecule is pulled away from z and eventually crosses the PBC. I took a good look at gmx-list and noticed that you rode conducting tests with this option. Could you give me a light on this problem too? Grateful eef _______________________________________ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br
> When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Constraint causing system to explode (Warren Gallin) > 2. PMF in vacuum ([email protected]) > 3. Re: Compile gromacs 4.0.7 with mopac (Stefan Hoorman) > 4. vibrational spectra of glucose (Nilesh Dhumal) > > > ------------------------------ > > Message: 2 > Date: Thu, 27 May 2010 12:12:03 -0400 > From: [email protected] > Subject: [gmx-users] PMF in vacuum > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear Eudes: > To answer your pbc vs no-pbc question, I suggest that you use pbc=no > and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all > interactions in direct space with no cutoffs. > > ## Major comments that you should still investigate > > 1. There is no need to use a virtual atom, the pull code will use the > center of mass. I strongly suggest that you stop using a virtual atom > and just use the entire benzene as an argument to the pull code group. > I have had difficulties with slightly more complicated setups of this > type. > > 2. In test2.jpg, the system without pbc shows a flat PMF after the > cut-off -- exactly what one would expect. The pbc system shows > continued interaction -- again what I would expect. So there is > nothing actually all that strange here. One would not expect to see > such a drastic difference in a high dielectric such as water, but in > vacuum I suspect that this is expected. > > 3. Please clarify what your cutoff was. I don't see a cut-off listed > in your .mdp options and leaving this to the default of 1.0 nm is a > bad idea because it can lead to confusion a times like this. I might > assume that it was 0.7 nm based on test2.jpg, but then see the point > #3 below. > > 4a. I have no idea what -DPOSRES is actually doing for you since I > can't see your topology. > > 4b. Are you sure that "pull_dim = N N Y" is really what you want? > Sometimes one wants to average over X and Y, but I am not sure that > you do in this case. > > 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? > > ### More minor notes: > > 5. regarding test1.jpg: a PMF is correct to an additive constant, > meaning that you can shift two PMFs relative to one another. These 2 > PMFs are therefore less different than they appear in your compaison > plot, but they do differ in the slope between 1.0 - 2.0 nm. This is > probably just a convergence issue and you will always need to do tests > like this. > > 6. regarding histo.png: can you confirm that the few very short > gaussians are due to less sampling in a few windows? In any event, the > overlap looks good. > > Chris > > -- original message -- > > Hello Chris, thanks for your attention. > I'm sending you some links to some tests > I performed. As I said you will notice that > depending on the parameter used my simulation > shows PMF profiles quite different. Especially what > concerns to the difference between the use or not of the PBC. > > https://sites.google.com/site/fileti/files/test1.jpg > https://sites.google.com/site/fileti/files/test2.jpg > https://sites.google.com/site/fileti/files/histo.png > > I have constructed two very similar topologies (ben-a.itp and ben-b.itp) > where I put a virtual site in the center of benzene. > This sites were restrained to keep my molecules > fixed distance desired. > > The basic details of the simulations are given below:1000 > > define = -DPOSRES > integrator = sd > tinit = 0 > dt = 0.002 > nsteps = 5000000 or 500000 > comm-mode = angular > nstcomm = 1 > comm-grps = System > bd-fric = 1 > ld-seed = 1993 > nstlist = 5 > ns_type = simple > pbc = no or xyz > periodic_molecules = no > rlist = 0 > coulombtype = Cut-off > vdw-type = Cut-off > rvdw = 0 > DispCorr = no > Tcoupl = Nose-Hoover > tc_grps = system > tau_t = 0.1 > ref_t = 300 > Pcoupl = no > pcoupltype = isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > constraints = all-bonds > constraint_algorithm = lincs > > ; COM PULLING > pull = umbrella > pull_geometry = distance > pull_dim = N N Y > pull_r1 = 1 > pull_r0 = 1.5 > pull_constr_tol = 1e-06 > pull_start = yes > pull_nstxout = 10 > pull_nstfout = 10 > pull_ngroups = 1 > pull_group0 = BENa > pull_weights0 = > pull_pbcatom0 = 0 > pull_group1 = BENb > pull_weights1 = > pull_pbcatom1 = 0 > pull_vec1 = 0 0 1 > pull_init1 = 0 > pull_rate1 = 0.0 > pull_k1 = 1700 or > > >
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