Re: [gmx-users] COM
He means, in your first email, your command is using fix.ndx and HAGD group is in your index.ndx, have you checked it? On Tue, Jan 22, 2019 at 7:54 PM laura O. wrote: > Hi, > > I already used index.ndx at the line of code but the error kept the same. I > believe this is not the problem > > Thanks > Laura > > Em ter, 22 de jan de 2019 às 16:25, Joaquim Rui de Castro Rodrigues < > joaquim.rodrig...@ipleiria.pt> escreveu: > > > Hi, > > > > Your command line specifies -n fix.ndx but you seem to be editing a file > > named "index.ndx". > > > > HTH, > > Rui Rodrigues > > > > > > De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> em nome de laura O. < > > laura.o.vendr...@gmail.com> > > Enviado: 22 de janeiro de 2019 17:31 > > Para: gromacs.org_gmx-users@maillist.sys.kth.se > > Assunto: [gmx-users] COM > > > > Dear Users. > > > > I'm trying to calculate the center of mass distance between > cyclodextrine ( > > HAGD) and a biological molecule (MTX). > > I've searched on gromacs documentation in gmx distance > > > > I use command line: > > gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav > > cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX". > > > > On the index file (index.ndx) the names are correct (transcribed at the > end > > of e-mail) > > > > However, I get the message bellow: > > Invalid index group reference(s) > > Cannot match 'group "HAGD"', because no such index group can be found. > > Cannot match 'group "MTX"', because no such index group can be found. > > > > > > Then, I used the index numbers for HAGD and MTX respectively. By doing > so, > > I got the graphic but with wrong and unexpected results. I look the > > trajectory in VMD. > > > > What could I be doing wrong? > > > > > > What is the exact command for calculation of center of mass distance > > calculation between two groups A & B have in my index? > > Doing by the dist pair I manage to get a good result, but since > > cyclodextrine is cone shaped, I don't think that using the center of mass > > would be the best option. > > > > > > Index.ndx: > > > > [ HAGD ] > >123456789 10 11 12 13 14 > 15 > > 16 17 18 19 20 21 22 23 24 25 26 27 28 29 > 30 > > 31 32 33 34 35 36 37 38 39 40 41 42 43 44 > 45 > > 46 47 48 49 50 51 52 53 54 55 56 57 58 59 > 60 > > 61 62 63 64 65 66 67 68 69 70 71 72 73 74 > 75 > > 76 77 78 79 80 81 82 83 84 85 86 87 88 89 > 90 > > 91 92 93 94 95 96 97 98 > > [ MTX ] > > 99 100 101 102 103 104 105 106 107 108 109 110 111 112 > 113 > > 114 115 116 117 118 119 120 121 122 123 124 125 126 127 > 128 > > 129 130 131 132 133 134 135 136 137 138 139 140 141 > > -- > > 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.
Re: [gmx-users] COM
Hi, I don't think you need a double quote in your select HAGD On Tue, Jan 22, 2019 at 6:32 PM laura O. wrote: > Dear Users. > > I'm trying to calculate the center of mass distance between cyclodextrine ( > HAGD) and a biological molecule (MTX). > I've searched on gromacs documentation in gmx distance > > I use command line: > gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav > cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX". > > On the index file (index.ndx) the names are correct (transcribed at the end > of e-mail) > > However, I get the message bellow: > Invalid index group reference(s) > Cannot match 'group "HAGD"', because no such index group can be found. > Cannot match 'group "MTX"', because no such index group can be found. > > > Then, I used the index numbers for HAGD and MTX respectively. By doing so, > I got the graphic but with wrong and unexpected results. I look the > trajectory in VMD. > > What could I be doing wrong? > > > What is the exact command for calculation of center of mass distance > calculation between two groups A & B have in my index? > Doing by the dist pair I manage to get a good result, but since > cyclodextrine is cone shaped, I don't think that using the center of mass > would be the best option. > > > Index.ndx: > > [ HAGD ] >123456789 10 11 12 13 14 15 > 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 > 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 > 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 > 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 > 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 > 91 92 93 94 95 96 97 98 > [ MTX ] > 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 > 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 > 129 130 131 132 133 134 135 136 137 138 139 140 141 > -- > 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.
Re: [gmx-users] Calculate potential as function of time
The total potential energy of the system is printed when you use g_energy (in your version) See Justin tutorial for example: http://www.mdtutorials.com/gmx/lysozyme/05_EM.html Best, On Mon, Jan 21, 2019 at 3:28 PM Indu Kumari wrote: > Good evening sir, > > Did you use this command? > > g_energy -f em.edr -o em.xvg > > When should I meet you sir, tomorrow? > > With regards, > *Indu Kumari* > > > On Mon, Jan 21, 2019 at 12:23 PM Rituraj Purohit > > wrote: > > > Hi Friends, > > How to get a "graph of potential as function of time" ?? Currently I am > > using gmx potential script to generate potential.xvg but it is showing > > potential as function of boxlength. > > reg > > Rituraj > > -- > > 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.
Re: [gmx-users] regarding editconf
Hi all, My point is when you center your solute at (0,0,0) there is a half of your solute will be placed at the quarter of negative coordinates. And then you add water, gmx solvate will only add water in positive coordinate region. Am I right? On Wed, Jan 16, 2019 at 5:19 AM Omkar Singh wrote: > My advice is that don't use many option in on shot. In place of -center try > by -translate with rotation. > > Best regard > > On Tue, Jan 15, 2019 at 8:52 PM Ali Khodayari < > ali.khoday...@student.kuleuven.be> wrote: > > > Thank you Justin. I try to search more for the reason. My best, Ali > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > On Behalf Of Justin > > Lemkul > > Sent: dinsdag 15 januari 2019 16:10 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] regarding editconf > > > > > > > > On 1/15/19 9:34 AM, Ali Khodayari wrote: > > > Thank you for your response Justin! > > > I don't really see how it can cause an error, while it might be just a > > > visualization defect in VMD. > > > Previously, I tried to perform each step separately, like doing a > > > centering by -center 0 0 0, but even performing this step leads to the > > error "step 0: > > > Water molecule starting at atom 40225 can not be settled." The only > > > difference would be a change in the coordinates, no? It is not due to > > > the fact that I am using 5.1.2 version, is it? > > > > Systems can become unstable for any number of reasons, but not simply > > because some part of a protein appears to be protruding into space. > > That's just normal PBC. > > > > 5.1.2 is very old but I don't know of any specific reason why it should > > cause a problem. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 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. > > > -- > 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.
