Hello Chris, thanks for the reply. Below his message commented walkthrough. In your email you asked me for quantitative results. All I have so far is a visual inspection of the pulling trajectory. All I can see are the two molecules moving linearly away from each other in a rectangular box of dimensions 3x3x6nm. However this separation does not occur on the z axis, as I wanted, but in a diagonal way across the faces of the box.
Bests eef > 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. Ok, now I'm using only the center of mass of the molecules, no virtual sites. > 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. Alright! In fact the well of both PMFs are not so different. > 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. Apesar de eu nao ter incluido o valor do cutoff na mensagem anterior eu usei 1.2 nm Although I have not included the cutoff value in previous message I used it as 1.2 nm. > 4a. I have no idea what -DPOSRES is actually doing for you since I > can't see your topology. A ideia de usar POSRES se referia ao emprego dos sitios virtuais. Assim eu restringia a distancia das moleculas atraves da restricao do sitios virtuais sobre seus centros. The idea of using POSRES is referred to the employment of the virtual sites. So I restricted the distance of molecules by restricting virtual sites on their centers. > > 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. I want to separate the two molecules from one another so that the displacement is restricted to the z axis. I can be wrong, but I think to do it in water, using PBC, I should use the components distance (N N Y ) with direction geometry to get a pulling in a direction z! Please correct me if it is wrong. > 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? Here they are worthless, because I have not used the option "cylinder". I should have removed these options from the original message. > ### 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. Surely. > 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. Yes, there were two histograms whose simulations had crashed for some reason. It was corrected. _______________________________________ 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 4. PMF in vacuum and pull direction ([email protected]) > > > > Message: 4 > Date: Tue, 08 Jun 2010 12:14:34 -0400 > From: [email protected] > Subject: [gmx-users] PMF in vacuum and pull direction > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear Eudes: > > This is better, but I'm afraid that I'm going to have to insist on > getting everything I asked for. Please see my previous message. > > Chris. > > -- original message -- > > Dear Chris, I'm so sorry for surperficial email. > You are correct because in the previous message > I forgot to mention that now the simulation was > performed in water (naturally with PBC). > The main parameters of the simulation are given below. > As I said, I wish to keep the displacement of the pulled molecule at > the z-axis, but I'm not getting with this protocol. > > For the vacuum I followed the tips you gave me earlier and had success! > Thanks > eef > > > > title = Umbrella pulling simulation > integrator = sd > dt = 0.002 > nsteps = 3000000 > constraint_algorithm = lincs > constraints = all-bonds > nstlist = 5 > ns_type = simple > rlist = 1.2 > rcoulomb = 1.2 > rvdw = 1.2 > coulombtype = Cut-off > Tcoupl = V-rescale > tc_grps = system > tau_t = 0.1 > ref_t = 298 > Pcoupl = no > pcoupltype = isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > pbc = xyz > > ; Pull code > pull = umbrella > pull_geometry = direction > pull_dim = N N Y > pull_start = yes > pull_ngroups = 1 > pull_group0 = BEN1 > pull_group1 = BEN2 > pull_vec1 = 0 0 1 > pull_rate1 = 0.001 > pull_k1 = 1600 > > > > > Message: 4 > > Date: Tue, 08 Jun 2010 08:05:23 -0400 > > From: chris.neale at utoronto.ca > > Subject: [gmx-users] PMF in vacuum and pull direction > > To: gmx-users at gromacs.org > > Message-ID: <20100608080523.i6oo62he1wwc0wkg at webmail.utoronto.ca> > > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > > format="flowed" > > > > Dear Eudes: > > > > You can make my job a whole lot easier! First, please go back through > > all of the comments that I gave you last time and reply to them one by > > one. Did you do them? What did you see? Second, please include your > > new .mdp and some quantitative results to better explain what you see > > (e.g. your .px file and a description of why the values are not what > > you expect). > > > > Sorry if this sounds annoying, but there's no point in my working in the > > dark. > > > > Chris. > > > > -- original message -- > > > > 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 > > > > > > Message: 2 > > Date: Thu, 27 May 2010 12:12:03 -0400 > > From: chris.neale at utoronto.ca > > Subject: [gmx-users] PMF in vacuum > > To: gmx-users at gromacs.org > > Message-ID: <20100527121203.orb2sq228s4ow0wg at webmail.utoronto.ca> > > 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 > > > > > > > > > > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 74, Issue 53 > ***************************************** >
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