To be clear, i put 30 similar AA around NT i want to know how the average distance of group PROTEIN( consist of 30 AA ) varies during 100nS simulation. As i see in .gro file this distance decreased. I mean at the first moment i put them about 3nm far from Z axis of NT. THIS 3NM IS THE MINIMUM LENGTH OF A LINE BETWEEN AA COM POINT AND Z AXIS OF NT, AS YOU CAN IMAGINE THIS LINE IS PERPENDICULAR TO Z AXIS OF NT. this length is decrease after 100nS. But what i can't understand is that when i analyze it by g_dist( i select ZnS(NT) and Group Potein(=30 AA) in g_dist).. this is the result!
Group 0 ( System) has 27831 elements Group 1 ( Other) has 408 elements Group 2 ( ZnS) has 408 elements Group 3 ( Protein) has 720 elements Group 4 ( Protein-H) has 390 elements Group 5 ( C-alpha) has 30 elements Group 6 ( Backbone) has 90 elements Group 7 ( MainChain) has 90 elements Group 8 ( MainChain+Cb) has 120 elements Group 9 ( MainChain+H) has 180 elements Group 10 ( SideChain) has 540 elements Group 11 ( SideChain-H) has 300 elements Group 12 ( Prot-Masses) has 720 elements Group 13 ( non-Protein) has 27111 elements Group 14 ( Water) has 26703 elements Group 15 ( SOL) has 26703 elements Group 16 ( non-Water) has 1128 elements Select a group: 2 Selected 2: 'ZnS' Select a group: 3 Selected 3: 'Protein' 0.0000000 0.2176011 -0.0120678 -0.0465498 0.2122209 1.0000000 0.2124534 -0.0301750 -0.0463870 0.2051198 2.0000000 0.1923753 -0.0158403 -0.0510135 0.1848106 3.0000000 0.1885315 -0.0107298 -0.0488160 0.1817856 4.0000000 0.2044982 -0.0052650 -0.0490329 0.1984630 5.0000000 0.2033602 -0.0002742 -0.0429537 0.1987720 6.0000000 0.2050487 0.0013833 -0.0444658 0.2001646 7.0000000 0.2002475 0.0041072 -0.0415003 0.1958568 8.0000000 0.2006473 0.0033450 -0.0511889 0.1939790 9.0000000 0.2032918 -0.0000119 -0.0330052 0.2005947 10.0000000 0.2255659 0.0003929 -0.0415857 0.2216990 11.0000000 0.2243811 0.0118313 -0.0344751 0.2214010 . . . 99990.0000000 0.6195676 -0.1357532 -0.0029635 0.6045051 99991.0000000 0.5355353 -0.3716600 0.0125020 0.3853707 99992.0000000 0.5243484 -0.3698001 0.0180452 0.3712997 99993.0000000 0.4459361 -0.1407223 -0.2021322 0.3717511 99994.0000000 0.5592619 -0.3545561 -0.2162843 0.3745463 99995.0000000 0.5707593 -0.3472078 -0.2309759 0.3896961 99996.0000000 0.5238984 -0.3467841 -0.0103419 0.3925600 99997.0000000 0.5122938 -0.3379052 0.0097873 0.3849275 99998.0000000 0.5608831 -0.3396225 -0.2052171 0.3963993 99999.0000000 0.5230988 -0.3479364 0.0172603 0.3902240 100000.0000000 0.5158455 -0.3283865 0.0047119 0.3977897 If the nanotube is along Z axis, so how g_dist calculate the COM of nano tube? Is it each point along Z axis which pass center of nano tube or COM in this case is just one point in the nanotube. If it is the second one, so g_dist doesn't calculate perpendicular distance from AA to Z axis... so it is completely different from what i want. How can i get what i want? this is exactly what want it is not an article it is just the figure 2 https://www.sciencedirect.com/science/article/pii/S0008622314006691#f0010 i'm completely confused! Please help me Best Rose On Wed, 7 Nov 2018, 18:32 Justin Lemkul <jalem...@vt.edu wrote: > > > On 11/3/18 2:15 PM, rose rahmani wrote: > > On Sat, 3 Nov 2018, 19:56 Justin Lemkul <jalem...@vt.edu wrote: > > > >> > >> On 11/2/18 11:36 AM, rose rahmani wrote: > >>> but this is output of -oall. its not a single value?! > >> You are asking in your command for all interatomic distances between the > >> groups (presumably, because you haven't shown your selection). This > >> command won't yield what you're hoping to see and my advice does not > >> apply for this type of situation (which doesn't seem to even match your > >> original statement of your problem). > >> > >>> gmx distance -f md2.xtc -oall dist.xvg -n index.ndx > >>> # gmx distance is part of G R O M A C S: > >>> # > >>> # > >>> > >> > ¸<8d><9a><9a><91>ÃÂ<9a><9b>ð<8d><9e><91><98><9a>ò<9e><98><9a><91><8b><9e>þ<85><8a><8d><9a>ü<86><9e><91>ì<94><86><9d><99a>8a><< > >>> # > >>> @ title "Distance" > >>> @ xaxis label "Time (ps)" > >>> @ yaxis label "Distance (nm)" > >>> @TYPE xy > >>> > >>> 1.000 0.229 0.229 0.446 0.582 0.446 0.229 > 0.446 > >>> 0.583 0.447 0.229 0.447 0.227 0.228 0.229 0.446 > >>> 0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447 > >>> 0.227 0.227 0.228 0.446 0.582 0.446 0.227 0.446 > >>> 0.583 0.447 0.227 0.447 0.227 0.228 0.229 0.446 > >>> 0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447 > >>> 0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446 > >>> 0.583 0.447 0.228 0.447 0.227 0.229 0.229 0.446 > >>> 0.582 0.446 0.229 0.446 0.583 0.447 0.229 0.447 > >>> 0.227 0.229 0.229 0.446 0.582 0.446 0.229 0.446 > >>> 0.583 0.447 0.229 0.447 0.227 0.228 0.229 0.446 > >>> 0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447 > >>> 0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446 > >>> 0.583 0.447 0.228 0.447 0.227 0.227 0.228 0.446 > >>> 0.582 0.446 0.227 0.446 0.583 0.447 0.227 0.447 > >>> 0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446 > >>> 0.583 0.447 0.228 0.4 > >>> . > >>> . > >>> . > >>> > >>> and this is -o of g_dist; > >>> g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg > >>> # > >>> # g_dist is part of G R O M A C S: > >>> # > >>> # GRowing Old MAkes el Chrono Sweat > >>> # > >>> @ title "Distance" > >>> @ xaxis label "Time (ps)" > >>> @ yaxis label "Distance (nm)" > >>> @TYPE xy > >>> @ view 0.15, 0.15, 0.75, 0.85 > >>> @ legend on > >>> @ legend box on > >>> @ legend loctype view > >>> @ legend 0.78, 0.8 > >>> @ legend length 2 > >>> @ s0 legend "|d|" > >>> @ s1 legend "d\sx\N" > >>> @ s2 legend "d\sy\N" > >>> @ s3 legend "d\sz\N" > >>> 0.0000000 0.2176011 -0.0120678 -0.0465498 0.2122209 > >>> 1.0000000 0.2124534 -0.0301750 -0.0463870 0.2051198 > >>> 2.0000000 0.1923753 -0.0158403 -0.0510135 0.1848106 > >>> 3.0000000 0.1885315 -0.0107298 -0.0488160 0.1817856 > >>> 4.0000000 0.2044982 -0.0052650 -0.0490329 0.1984630 > >>> 5.0000000 0.2033602 -0.0002742 -0.0429537 0.1987720 > >>> 6.0000000 0.2050487 0.0013833 -0.0444658 0.2001646 > >>> 7.0000000 0.2002475 0.0041072 -0.0415003 0.1958568 > >>> 8.0000000 0.2006473 0.0033450 -0.0511889 0.1939790 > >>> 9.0000000 0.2032918 -0.0000119 -0.0330052 0.2005947 > >>> 10.0000000 0.2255659 0.0003929 -0.0415857 0.2216990 > >>> 11.0000000 0.2243811 0.0118313 -0.0344751 0.2214010 > >>> 12.0000000 0.2347855 0.0078275 -0.0383532 0.2314994 > >>> 13.0000000 0.2371541 0.0081918 -0.0388267 0.2338107 > >> Here, you have what you want (I assume), and the first column after the > >> time is all you need. It's the distance, which also can't be negative > >> because it is the magnitude of the vector length and is unsigned. > >> > > How S0 is calculated? Does it resulted from distance between COM of amino > > acid and COM of tube? Although, it is the magnitude of ... but it's > > The distance you get is the distance you ask for in your selection > (which isn't shown or stated). The distance formula is quite simple, > consult any geometry textbook. > > > calculated from x,y,z which may be negative and were not abaolute?! In > > addition, i put AAs (more than) 1.5 nm far from tube as an initial > > configuration, but any 1.5 nm distance..??? > > > > A component of a vector may be positive or negative, these are just > differences along x, y, and z. The total length of a vector is a > magnitude and is therefore positive. > > -Justin > > > > >> -Justin > >> > >>> . > >>> . > >>> . > >>> > >>> > >>> On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul <jalem...@vt.edu> wrote: > >>> > >>>> On 11/1/18 2:25 PM, rose rahmani wrote: > >>>>> I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be > >>>>> multiplied by (-), but how should i modify second column,i don't know > >> how > >>>>> s0 is calculated by g_distance to modify it?? > >>>> The output of -oall is a single value, the actual distance, which I > >>>> assume is what you are talking about in your previous message. You can > >>>> parse that column in any scripting language you like and > >>>> > >>>> [ pseudocode, not functional ] > >>>> if (value < 0) > >>>> { > >>>> value *= -1 > >>>> } > >>>> > >>>> -Justin > >>>>> On Wed, 31 Oct 2018, 19:38 Justin Lemkul, <jalem...@vt.edu> wrote: > >>>>> > >>>>>> On 10/31/18 12:06 PM, rose rahmani wrote: > >>>>>>> Hi, > >>>>>>> > >>>>>>> I want to calculate distances between fixed tube in the middle of > the > >>>> box > >>>>>>> and amino acids(all are same type)around it. But gmx distance gives > >> me > >>>>>> the > >>>>>>> relative distance i mean AA can be front or back( can be 0.5 or > -0.5 > >>>> from > >>>>>>> tube) of tube but still |-0.5|=0.5 nm far from it. How can i have > >> the > >>>>>>> absolute value of distances? > >>>>>>> Would you please help me? > >>>>>> Write a simple post-processing script that multiplies any negative > >> value > >>>>>> by -1. > >>>>>> > >>>>>> -Justin > >>>>>> > >>>>>> -- > >>>>>> ================================================== > >>>>>> > >>>>>> Justin A. Lemkul, Ph.D. > >>>>>> Assistant Professor > >>>>>> Virginia Tech Department of Biochemistry > >>>>>> > >>>>>> 303 Engel Hall > >>>>>> 340 West Campus Dr. > >>>>>> Blacksburg, VA 24061 > >>>>>> > >>>>>> jalem...@vt.edu | (540) 231-3129 > >>>>>> http://www.thelemkullab.com > >>>>>> > >>>>>> ================================================== > >>>>>> > >>>>>> -- > >>>>>> 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. > >>>>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Virginia Tech Department of Biochemistry > >>>> > >>>> 303 Engel Hall > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> jalem...@vt.edu | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> ================================================== > >>>> > >>>> -- > >>>> 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. > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Virginia Tech Department of Biochemistry > >> > >> 303 Engel Hall > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> 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. > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.