Thank you Benson Muite and Bratin Kumar for replying. I am using version 5.1.1. Thanks Bratin for pointing that out, now it works when the file was transferred to the working directory!
________________________________ From: [email protected] <[email protected]> on behalf of [email protected] <[email protected]> Sent: Friday, November 2, 2018 3:51 PM To: [email protected] Subject: gromacs.org_gmx-users Digest, Vol 175, Issue 9 Send gromacs.org_gmx-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: Gmx distance (rose rahmani) 2. Opening PDB files in GROMACS on Windows using Cygwin (Neena Susan Eappen) 3. Re: Opening PDB files in GROMACS on Windows using Cygwin (Benson Muite) 4. Re: Opening PDB files in GROMACS on Windows using Cygwin (Bratin Kumar Das) ---------------------------------------------------------------------- Message: 1 Date: Fri, 2 Nov 2018 19:06:36 +0330 From: rose rahmani <[email protected]> To: [email protected] Subject: Re: [gmx-users] Gmx distance Message-ID: <CAO6==5tpaj+he1jzqkxqsckzun4oqjbxvpbntoewup0xcvk...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" but this is output of -oall. its not a single value?! 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>???<9a><9b>???<8d><9e><91><98><9a>???<9e><98><9a><91><8b><9e>???<85><8a><8d><9a>???<86><9e><91>???<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 . . . On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul <[email protected]> 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, <[email protected]> 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 > >> > >> [email protected] | (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 [email protected]. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > [email protected] | (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 [email protected]. ------------------------------ Message: 2 Date: Fri, 2 Nov 2018 15:45:44 +0000 From: Neena Susan Eappen <[email protected]> To: "[email protected]" <[email protected]> Subject: [gmx-users] Opening PDB files in GROMACS on Windows using Cygwin Message-ID: <yqbpr0101mb2097a16098099044af4790f7cd...@yqbpr0101mb2097.canprd01.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hello GROMACS users, I am a first time user of GROMACS. According to this excellent tutorial (http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html), I downloaded the PDB file for lyzozyme, then removed water molecules, typed in the following command on CygwinShell (with GROMACS activated). $ gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce However, I get an error saying: In command line option -f, file 1AKI_clean.pdb does not exit or is not accessible. Please advice where am I going wrong. Any insight would be appreciated. Many thanks, Neena Eappen Graduate Student Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T ------------------------------ Message: 3 Date: Fri, 2 Nov 2018 15:48:25 +0000 From: Benson Muite <[email protected]> To: "[email protected]" <[email protected]> Subject: Re: [gmx-users] Opening PDB files in GROMACS on Windows using Cygwin Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" What version of GROMACS are you using? On 11/2/18 5:45 PM, Neena Susan Eappen wrote: > Hello GROMACS users, > > > I am a first time user of GROMACS. According to this excellent tutorial > (http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html), I downloaded the > PDB file for lyzozyme, then removed water molecules, typed in the following > command on CygwinShell (with GROMACS activated). > > $ gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce > > However, I get an error saying: > > In command line option -f, file 1AKI_clean.pdb does not exit or is not > accessible. > > Please advice where am I going wrong. Any insight would be appreciated. > > Many thanks, > > Neena Eappen > Graduate Student > Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T ------------------------------ Message: 4 Date: Fri, 2 Nov 2018 21:21:26 +0530 From: Bratin Kumar Das <[email protected]> To: [email protected] Subject: Re: [gmx-users] Opening PDB files in GROMACS on Windows using Cygwin Message-ID: <CAM7TW5t_k8b_bU4P1fiSnJ2B75=e6ge7pu4pbptwxaof+xm...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" What ever version you use if the file is not present in your working directory ..it will give the same error On Fri, Nov 2, 2018, 9:18 PM Benson Muite <[email protected]> wrote: > What version of GROMACS are you using? > > On 11/2/18 5:45 PM, Neena Susan Eappen wrote: > > Hello GROMACS users, > > > > > > I am a first time user of GROMACS. According to this excellent tutorial ( > http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html), I downloaded > the PDB file for lyzozyme, then removed water molecules, typed in the > following command on CygwinShell (with GROMACS activated). > > > > $ gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce > > > > However, I get an error saying: > > > > In command line option -f, file 1AKI_clean.pdb does not exit or is not > accessible. > > > > Please advice where am I going wrong. Any insight would be appreciated. > > > > Many thanks, > > > > Neena Eappen > > Graduate Student > > Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T > -- > 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 [email protected]. > ------------------------------ -- 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 [email protected]. End of gromacs.org_gmx-users Digest, Vol 175, Issue 9 ***************************************************** -- 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 [email protected].
