Dear Chris, thank you for help. I performed the test you suggested, with no pressure coupling. Note that the behavior of the profile remained the same even with no pressure coupling. https://goo.gl/photos/2d8tsYFwp2eHCuCWA
The simulation parameters were exactly the same (except the sampling in the test was 5 ns window and by coupling pressure, which was turned off). Bests eef _______________________________________ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ > ------------------------------ > > Message: 2 > Date: Sun, 26 Jul 2015 02:45:50 +0000 > From: Christopher Neale <chris.ne...@alum.utoronto.ca> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 > (Eudes Fileti) > Message-ID: > < > blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Eudes: > > Glad that you solved one of the two issues. As for the bumps in the PMF, I > have a new theory: the bumps come from pressure coupling. When the sampled > distance, d, between the two molecules fluctuate a little closer than the > center of restraint, d0, that adds a repulsive force that contributes to > the virial and the box gets a little larger. Conversely, slight > fluctuations of d that are larger than d0 will add a small bias to box > contraction. This should be more noticeable when the restrained distance > involves larger masses. > > It is at the moment unclear to me whether this might exert an effect > indirectly due to overall system density or more directly as coordinate > scaling impacts the instantaneous value of d. If it is the latter, then > semi-isotropic pressure coupling, may also enhance the effect since the > virial will be computed independently along the order parameter (I presume) > and hence there is less noise from other dimensions. > > Can you please try again without pressure coupling (single precision > should be fine for this test). Hopefully this is not the source of the > bumps because, if it is affecting the PMF noticeably and the underlying > free energy surface has a large gradient, then d will always be on one side > of d0 and the effect will not be merely bumps but also some type of bias in > the PMF. Whether this bias is accurate or artifactual falls outside of my > mathematical abilities. The thing is, the force is a real force between > real atoms so it seems like it really should be included in the virial (as > it certainly is... I checked). I can tell you one thing for sure: the > effect on box volume is real and noticeable. That is, if you look at the > average system volume when d<<d0, it differs in a statistically significant > manner from the average system volume when d>>d0 (something that I also > checked). > > Thank you for looking into this further, > Chris. > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Eudes > Fileti <fil...@gmail.com> > Sent: 24 July 2015 16:47 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 > (Eudes Fileti) > > Hello Chris, I write to report the results of the tests you suggested. > To recap, I have two problems to solve. 1) The bad sampling around z = 0 > and 2) the bumps along to the profile. > > I solved the first discarding all the my initial configurations and > performing a new pulling (SMD). Only this time I used a higher force > constant (5000 kJ/mol nm2). Thus I got configurations close to z = 0, where > they were not generated. > > For the second problem, you suggested recalculate the PMF using double > precision. The results of this test showed that it does not solve the > problem, on the contrary the bumps were even more pronounced, as indicated > by the plot in this link. https://goo.gl/photos/wGNhdyNG9pdqGfcB6 > > All tests were performed with prototypes simulations, with 40 windows of 2 > ns spaced by 0.1 nm. A larger sample is obviously necessary for reliable > profiles, but this was enough to show the trend that I wanted to watch. > > As I have mentioned before, I've done several tests aiming to eliminate > these bumps: use of higher sampling, up to 20ns per window; reducing the > spacing between the windows (from 0.1 to 0.05 nm); changing the spring > constant from 1000 up to 5000 kJ/mol nm2, use of two different versions of > the Gromacs (4.6 e 5.0) and also I tested it with two different sets of > initial settings. > > None of this attempts solved the bumps problem. > > If you (or someone else) have any other tips please let me know. > > Thank you > eef > > _______________________________________ > Eudes Eterno Fileti > Instituto de Ci?ncia e Tecnologia da UNIFESP > Rua Talim, 330, S?o Jos? dos Campos - SP > P?gina: sites.google.com/site/fileti/ > > > > > ------------------------------ > > > > Message: 4 > > Date: Wed, 22 Jul 2015 14:56:50 +0000 > > From: Christopher Neale <chris.ne...@alum.utoronto.ca> > > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > > Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 > > Message-ID: > > < > > > blupr03mb18470a33a4e3ff149c95963c5...@blupr03mb184.namprd03.prod.outlook.com > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Eudes: > > > > There are two issues: The first issue is the fact that you've got a > > sampling problem near the bilayer center. The second issue is the > periodic > > bumps that you see in your PMFs. I'll take the second part first. > > > > The source of the periodic bumps in PMFs from umbrella sampling is, to > me, > > a million dollar question. I've seen them in my own work. I've seen then > in > > the literature (as you noted for Fig. 4 in > > http://www.mdpi.com/1422-0067/13/11/14451/htm ). I've seen them when > > people use g_wham and Alan Grossfield's version of WHAM. What I don't yet > > know is if people also see this when running US simulations with AMBER, > > CHARMM, or NAMD. Frankly, either answer scares me a little. If you see > wild > > oscillations of the PMF, at large distances then one possible source is > > that you are near a distance that is half your box length along the order > > parameter. Note that with constant pressure simulations you will get > > oscillations in the length of the box and also when your membrane changes > > shape it could flip the vector of closest approach by 180 deg if you are > > close to the half-box limit. However, that should not be relevant to the > > bumps (out of interest, how large is your box along z?). Although I do > > n't know what is going on with these PMF bumps, I also note that > > membranes as a whole always tend to migrate toward positive z and lipids > > tend to flow to positive x in gromacs simulations, so I wonder if it is a > > rounding issue. Could you try again with double precision and see if you > > get the bumps? > > > > As for the problem with sampling near the bilayer center... my first > guess > > is that you've got some of your replicas on the wrong side of the > bilayer's > > center. Did you intend to go across the center and sample also in the > lower > > leaflet? I've only ever used gromacs 3 and 4 to do pulling simulations, > > never gmx 5. You can see my concerns about gmx5 for this type of issue > near > > the bilayer center here: > > > https://www.mail-archive.com/gromacs.org_gmx-users%40maillist.sys.kth.se/msg11324.html > > One simply has to test it. However, if gmx5 does indeed work properly > with > > this new US philosophy, then I presume that you simply need to move your > > starting coordinates such that your solute is in the positive leaflet for > > all replicas. You can test this by visualization or g_dist, which reports > > the sign of the displacement (look in the 5th column I think for the z > > value). Note that you are using pull_start=yes, so which side of the > > bilayer your solute is initially on should make a difference here. > > > > Chris. > > > > -- original message: > > > > Hi Chris, a few days ago I posted a question on GMX list but > unfortunately > > I not received an answer yet. So I write to you for help at your > > convenience. > > http://permalink.gmane.org/gmane.science.biology.gromacs.user/78439 > > > > Besides the problem exposed the link above I'm trying to understand the > > importance of the relative distance between the COM. Due to fluctuation > in > > the position of the center of mass position of the membrane, the minimum > > distance is never zero, as shown in the graphs of my pulling below. What > is > > the effect of this difference in the calculation of the PMF? Could this > be > > the source of my problem? > > https://goo.gl/photos/cwwLzog6wXAgVJG88 > > > > Bests > > eef > > > > PS. I found this paper below where authors have published this unusual > > behavior (Figure 4). They did not explain the reason for the oscillations > > at large distances and I also do not know why this occurs. > > http://www.mdpi.com/1422-0067/13/11/14451/htm > > > > > > > > ________________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Eudes > > Fileti <fil...@gmail.com> > > Sent: 18 July 2015 21:06 > > To: gmx-us...@gromacs.org > > Subject: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 > > > > Hello guys, I'm trying to calculate the PMF using umbrella sampling for a > > small molecule to penetrate a lipid membrane. The 1D reaction coordinate > is > > along the z axis, which corresponds to the bilayer normal. The umbrella > > potential acts on the center of mass of the molecule. The initial > > configurations for each window, separated by a distance of 0.1nm, in a > > range of 4 nm (distance between the centers of mass of the membrane and > the > > molecule), were obtained by a SMD. > > > > The umbrella potential was applied according to the parameters below (for > > Gromacs version 5.0.3). Each window was sampled by 5 ns. > > > > ; COM PULLING > > pull = umbrella > > pull_geometry = direction > > pull_dim = N N Y > > pull_start = yes > > pull-print-reference = no > > pull_nstxout = 1000 > > pull_nstfout = 1000 > > pull_ngroups = 2 > > pull-ncoords = 1 > > ; Group name, weight (default all 1), vector, init, rate (nm/ps), > > kJ/(mol*nm^2) > > pull-group1-name = DPPC ; ref > > pull-group2-name = LIG ; pulled > > pull-coord1-groups = 1 2 > > pull-coord1-origin = 0 0 0 > > pull-coord1-vec = 0 0 1 > > pull-coord1-init = 0 > > pull-coord1-rate = 0.0 > > pull-coord1-k = 3000 > > > > Histograms and the PMF obtained are shown in figure the link below. > > https://goo.gl/photos/RkW9gbWrgeKEfV3R7 > > > > I repeated the same test using other parameters (larger and small k > values) > > and options (cylinder and position, for this later I have used gmx 4.6) > and > > so far I could not get a satisfactory profile. In all tests, a problem > that > > I have observed is that the region near z = 0 is not sampled (there is a > > gap between 0.0 and 0.5 nm). In addition the profile presents not smooth, > > but somehow oscillating mainly for large z. > > > > As the gmx distance give a value different of zero for the smallest > > distance of separation between the centers of mass (around 0.1-0.2 nm) I > > believe that this weird behavior is related to the reference distance > that > > I have used. > > > > Could someone give me a light? Most of the tips I read in GMX list are > > related to previous versions of the Gromacs and in a way the other tips > > were already included in my tests. > > > > Thank you > > eef > > > > _______________________________________ > > Eudes Eterno Fileti > > Instituto de Ci?ncia e Tecnologia da UNIFESP > > Rua Talim, 330, S?o Jos? dos Campos - SP > > P?gina: sites.google.com/site/fileti/ > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > ------------------------------ > > Message: 3 > Date: Sun, 26 Jul 2015 10:15:51 +0100 > From: Dawid das <add...@googlemail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Default cut-off scheme. > Message-ID: > < > cakslqn60ybuxhudjbgndfdsm1cag4oqufgebcz4hg7xigjz...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Actually, I am working with Gromacs 4.6.7, but thank you for a tip ;). > I forgot about the actual manual. > > All the best, > > Dawid Grabarek > > 2015-07-25 23:44 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>: > > > On Sun, Jul 26, 2015 at 12:32 AM Tamisra Pal <tamisra1...@gmail.com> > > wrote: > > > > > Hi , > > > > > > The cutoff-scheme by default is Verlet , unless you specify it as > group. > > > Yes , in this case , the ns_type is grid > > > > > > > ... assuming this is version 5. But Dawid will get an accurate answer > much > > faster by consulting the manual for the version he is using ;-) > > > > Mark > > > > > > > On Sun, Jul 26, 2015 at 1:33 AM, Dawid das <add...@googlemail.com> > > wrote: > > > > > > > Dear Gromacs Experts, > > > > > > > > I was issued with following minimize.mdp file: > > > > > > > > ; Minimization of bovine pancreatic trypsin inhibitor > > > > title = minimization of BPTI > > > > ; this is a comment > > > > integrator = l-bfgs ; (other: cg, l-bfgs) > > > > emtol = 500 ; convergence criterium- maximum value > > of > > > > force [kJ/(mol*nm)] > > > > emstep = 0.01 ; initial step size [nm] > > > > nsteps = 2000 ; number of steps > > > > nstlist = 1 ; frequency update of neighbour list > > > > ns_type = grid ; algorithm of updating neighbour > list. > > > It > > > > seems to be cell list method. > > > > nstenergy = 50 ; > > > > rlist = 1.0 > > > > coulombtype = PME > > > > rcoulomb = 1.0 > > > > rvdw = 1.0 > > > > pbc = xyz > > > > > > > > my question is what is the default cutoff-scheme here? group or > > Verlet? I > > > > assume there has to be default option because otherwhise nstlist and > > > > ns_type will not make sense, won't they? > > > > The other question is whether I understand ns_type=grid correctly. Is > > it > > > > cell list method as I commented? > > > > > > > > Best wishes, > > > > > > > > Dawid Grabarek > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > -- > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 135, Issue 136 > ******************************************************* > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
