RE: [gmx-users] qasi-harmonic entropy calculation
Hi Pedro, I am using 4565.9 as a conversion factor. I dont see any problem unless any condtion I needed to satisfy during the simulation. Simulation gave the result what I had expected. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro Sent: Thu 18/10/2007 8:57 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Maybe there has been some mistake during your calculations? No, g_covar gives the average covariance matrix. You can check this matrix with the command -ascii. If you have used your own program to calculate entropy double check units conversion stuff. Regards. Pedro. 2007/10/18, Naser, Md Abu <[EMAIL PROTECTED]>: > > Hi Pedro, > > Thank you for your attention to my email. Yes, I am using Schlitter > equation and the > rusult is cumulative. The entropy is meant to be decreased as the protein > is stick > on to a surface. > > I have used the entire protein as a subset. Is the programme takes the > final structure > for calculating covariance? > > With regards, > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > > -Original Message- > From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo > Gomes Lapido Loureiro > Sent: Thu 18/10/2007 1:47 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] qasi-harmonic entropy calculation > > Hi, > > I understand you are using the Schlitter equation, is that so? > Could you give more details? Such as, what subset of atoms are you using > to > calculate the entropy? Are you calculating it in dt time frames or are > your > results cumulative? Why do you expect the entropy to decrease? > > Regards, > > Pedro. > > > 2007/10/18, Naser, Md Abu <[EMAIL PROTECTED]>: > > > > Hi all user, > > > > I have calculated entroy over time from eigenvalue(g_covar) and > > the result shows that the entropy decreasing towards zeo. The results > > is ok as far as it decreases. But I do not understand why it is > > approaching > > to zero towards the end of the simulation. Can anyone explain why? > > > > I would appreciate your response. > > > > > > With regards, > > Abu Naser > > > > School Of Life Sciences > > Heriot-Watt University > > Edinburgh EH14 4AS > > Email: [EMAIL PROTECTED] > > Phone: +44(0)1314518265 > > Fax : +44(0) 131 451 3009 > > > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] qasi-harmonic entropy calculation
Hi David, Thanks for your information and I will have a look CVS head version. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 18/10/2007 4:18 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: > Hi, > > I understand you are using the Schlitter equation, is that so? > Could you give more details? Such as, what subset of atoms are you using > to calculate the entropy? Are you calculating it in dt time frames or > are your results cumulative? Why do you expect the entropy to decrease? > > Regards, > The CVS head version of g_anaeig computes these values as well. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] qasi-harmonic entropy calculation
Hi Pedro, Thank you for your attention to my email. Yes, I am using Schlitter equation and the rusult is cumulative. The entropy is meant to be decreased as the protein is stick on to a surface. I have used the entire protein as a subset. Is the programme takes the final structure for calculating covariance? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro Sent: Thu 18/10/2007 1:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu <[EMAIL PROTECTED]>: > > Hi all user, > > I have calculated entroy over time from eigenvalue(g_covar) and > the result shows that the entropy decreasing towards zeo. The results > is ok as far as it decreases. But I do not understand why it is > approaching > to zero towards the end of the simulation. Can anyone explain why? > > I would appreciate your response. > > > With regards, > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] qasi-harmonic entropy calculation
Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] make_ndx
Thanks XAvier and David! I think I know what I need to do to get my group. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 27/09/2007 7:29 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx Naser, Md Abu wrote: > Thanks david! > oops I misread. Sidechains do not contain C-alpha (which you can easily check in the index file). So within make_ndx type h for help on joining the two. > > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > > -Original Message- > From: [EMAIL PROTECTED] on behalf of David van der Spoel > Sent: Thu 27/09/2007 7:17 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] make_ndx > > Naser, Md Abu wrote: > > Hi XAvier, > > > > "Single out" I mean pick up only the side chain bonded with alpha > > carbon atom and > > put them in a group using make_ndx. > > > all side chains are. > and sidechain is a default group. > > > With regards, > > > > > > Abu Naser > > > > School Of Life Sciences > > Heriot-Watt University > > Edinburgh EH14 4AS > > Email: [EMAIL PROTECTED] > > Phone: +44(0)1314518265 > > Fax : +44(0) 131 451 3009 > > > > > > > > > > > > > > -Original Message----- > > From: [EMAIL PROTECTED] on behalf of Xavier Periole > > Sent: Wed 26/09/2007 8:42 PM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] make_ndx > > > > On Wed, 26 Sep 2007 20:08:06 +0100 > > "Naser, Md Abu" <[EMAIL PROTECTED]> wrote: > > > Hi All User, > > > > > > Is there anyway I can single out side chain of alpha carbon atom using > > >make_ndx? > > > > What do you mean by "single out" > > and with "side chain of alpha carbon" ? > > > > > > > > Thanks in advance. > > > > > > Abu Naser > > > > > > School Of Life Sciences > > > Heriot-Watt University > > > Edinburgh EH14 4AS > > > Email: [EMAIL PROTECTED] > > > Phone: +44(0)1314518265 > > >Fax : +44(0) 131 451 3009 > > > > > > > > > > > > > > > > - > > XAvier Periole - PhD > > > > 1- Institute of Molecular Assemblies > > City University of New York - USA > > 2- Molecular Dynamics-Group > > University of Groningen - The Netherlands > > http://md.chem.rug.nl/~periole > > - > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://
RE: [gmx-users] make_ndx
Thanks david! Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 27/09/2007 7:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx Naser, Md Abu wrote: > Hi XAvier, > > "Single out" I mean pick up only the side chain bonded with alpha > carbon atom and > put them in a group using make_ndx. > all side chains are. and sidechain is a default group. > With regards, > > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > > -Original Message- > From: [EMAIL PROTECTED] on behalf of Xavier Periole > Sent: Wed 26/09/2007 8:42 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] make_ndx > > On Wed, 26 Sep 2007 20:08:06 +0100 > "Naser, Md Abu" <[EMAIL PROTECTED]> wrote: > > Hi All User, > > > > Is there anyway I can single out side chain of alpha carbon atom using > >make_ndx? > > What do you mean by "single out" > and with "side chain of alpha carbon" ? > > > > > Thanks in advance. > > > > Abu Naser > > > > School Of Life Sciences > > Heriot-Watt University > > Edinburgh EH14 4AS > > Email: [EMAIL PROTECTED] > > Phone: +44(0)1314518265 > >Fax : +44(0) 131 451 3009 > > > > > > > > > > - > XAvier Periole - PhD > > 1- Institute of Molecular Assemblies > City University of New York - USA > 2- Molecular Dynamics-Group > University of Groningen - The Netherlands > http://md.chem.rug.nl/~periole > - > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] make_ndx
Hi XAvier, "Single out" I mean pick up only the side chain bonded with alpha carbon atom and put them in a group using make_ndx. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Wed 26/09/2007 8:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx On Wed, 26 Sep 2007 20:08:06 +0100 "Naser, Md Abu" <[EMAIL PROTECTED]> wrote: > Hi All User, > > Is there anyway I can single out side chain of alpha carbon atom using >make_ndx? What do you mean by "single out" and with "side chain of alpha carbon" ? > > Thanks in advance. > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 >Fax : +44(0) 131 451 3009 > > > > - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make_ndx
Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_dist
Hi XAvier, Yes, now it makes sense. Thank you very much for making it clear. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Tue 25/09/2007 8:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dist The output of g_dist gives: time distance DeltaX DeltaY DeltaZ distance = sqrt(DeltaX**2+DeltaY**2+DeltaZ**2) DeltaX, Y or Z are the differences of the atomic (COM) positions in each direction. A negative value simply means that one of the atoms (COM) has a value larger than the other one in the corresponding direction. The negative value is not a distance yet! Just the difference between the two atoms (COM) positions on one direction. Would that make sense? > hi XAvier, > > Thanks for your response. > It was a question more of about how you would interpret the > negative values(distance) in a particular component. > > With thanks, > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 >Fax : +44(0) 131 451 3009 > > > > > > > -Original Message- >From: [EMAIL PROTECTED] on behalf of Xavier Periole > Sent: Tue 25/09/2007 10:13 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] g_dist > > On Tue, 25 Sep 2007 10:03:30 +0100 > "Naser, Md Abu" <[EMAIL PROTECTED]> wrote: >> Hi David, >> >> Yes, it should be a vector as it is a difference between the center of mass >>of two groups in >> x,y, and z directions. Then, negative means an opposite direction. Is that >>right? > > g_dist gives the distance and the component in each direction. > The components been the difference between the atomic (or COM) > positions there is no problem in having a negative value. > >> >> Abu Naser >> >> School Of Life Sciences >> Heriot-Watt University >> Edinburgh EH14 4AS >> Email: [EMAIL PROTECTED] >> Phone: +44(0)1314518265 >>Fax : +44(0) 131 451 3009 >> >> >> >> >> >> >> -Original Message- >>From: [EMAIL PROTECTED] on behalf of David van der Spoel >> Sent: Tue 25/09/2007 9:42 AM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] g_dist >> >> Naser, Md Abu wrote: >>> >>> >>> Hi all user, >>> >>> I have just calculated a distance between backbone and side chain of the >>> same protein. I get >>> negative distance along x and y direction. What dose negative distance mean? >>> >> please be more specific. is that a vector? >> >>> Thanks in advance. >>> >>> >>> Abu Naser >>> >>> School Of Life Sciences >>> Heriot-Watt University >>> Edinburgh EH14 4AS >>> Email: [EMAIL PROTECTED] >>> Phone: +44(0)1314518265 >>> Fax : +44(0) 131 451 3009 >>> >>> >>> >>> >>> >>> >>> >>> ___ >>> gmx-users mailing listgmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- >> David van der Spoel, Ph.D. >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >> [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > - > XAvier Periole - PhD > > 1- Institute of Molecular Assemblies > City University of New York - USA > 2- Molecul
RE: [gmx-users] g_dist
hi XAvier, Thanks for your response. It was a question more of about how you would interpret the negative values(distance) in a particular component. With thanks, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Tue 25/09/2007 10:13 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dist On Tue, 25 Sep 2007 10:03:30 +0100 "Naser, Md Abu" <[EMAIL PROTECTED]> wrote: > Hi David, > > Yes, it should be a vector as it is a difference between the center of mass >of two groups in > x,y, and z directions. Then, negative means an opposite direction. Is that >right? g_dist gives the distance and the component in each direction. The components been the difference between the atomic (or COM) positions there is no problem in having a negative value. > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 >Fax : +44(0) 131 451 3009 > > > > > > > -Original Message- >From: [EMAIL PROTECTED] on behalf of David van der Spoel > Sent: Tue 25/09/2007 9:42 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] g_dist > > Naser, Md Abu wrote: >> >> >> Hi all user, >> >> I have just calculated a distance between backbone and side chain of the >> same protein. I get >> negative distance along x and y direction. What dose negative distance mean? >> > please be more specific. is that a vector? > >> Thanks in advance. >> >> >> Abu Naser >> >> School Of Life Sciences >> Heriot-Watt University >> Edinburgh EH14 4AS >> Email: [EMAIL PROTECTED] >> Phone: +44(0)1314518265 >> Fax : +44(0) 131 451 3009 >> >> >> >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_dist
Hi David, Yes, it should be a vector as it is a difference between the center of mass of two groups in x,y, and z directions. Then, negative means an opposite direction. Is that right? Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Tue 25/09/2007 9:42 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dist Naser, Md Abu wrote: > > > Hi all user, > > I have just calculated a distance between backbone and side chain of the > same protein. I get > negative distance along x and y direction. What dose negative distance mean? > please be more specific. is that a vector? > Thanks in advance. > > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dist
Hi all user, I have just calculated a distance between backbone and side chain of the same protein. I get negative distance along x and y direction. What dose negative distance mean? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_energy -fee -inf problem
Thanks Mark for pointing out my error. I will do it accordingly. With best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Mon 24/09/2007 9:22 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi Mark, > > The reacton shuld occur as: R-S-S-R + 2H+ -> 2R-SH. So at the very least, your "after" topology will need to have these hydrogens... You can't just cleave the S-S bond out of the .top and expect it to work. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_energy -fee -inf problem
Hi Mark, The reacton shuld occur as: R-S-S-R + 2H+ -> 2R-SH. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Mon 24/09/2007 9:02 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi Mark, > > Thank you very much for your replay.I was just trying to > calculate free energy difference between reduced protein and non-reduced > protein solvated in water(spc) using ffG43a2 force field. OK, so other than bond cleavage, what happens to the sulfurs when you reduce them in a real system? Mark > -Original Message- > From: [EMAIL PROTECTED] on behalf of Mark Abraham > Sent: Sat 22/09/2007 6:05 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] g_energy -fee -inf problem > > Naser, Md Abu wrote: > > Hi All User, > > > > I am getting free energy difference -inf. > > 1st I run a protein in water molecule and then I made a different > > topology file with deleting 4 disulfide bonds and accordingly the > angles and > > diherdal angles. > > What physical model are you trying to reproduce here? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_energy -fee -inf problem
Hi Mark, Thank you very much for your replay.I was just trying to calculate free energy difference between reduced protein and non-reduced protein solvated in water(spc) using ffG43a2 force field. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Sat 22/09/2007 6:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi All User, > > I am getting free energy difference -inf. > 1st I run a protein in water molecule and then I made a different > topology file with deleting 4 disulfide bonds and accordingly the angles and > diherdal angles. What physical model are you trying to reproduce here? > Then, I run -rerun for the both and and g_energy -fee, > which > giving me free energy difference -inf. > > Can anyone please point me out where I am making mistakes. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] atom index number
Hi Erik, Thank you very much for responding my query. I will try doing it using grep, awk and cut. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Erik Marklund Sent: Sat 22/09/2007 11:14 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] atom index number Hi, With less than 10 atoms, making an index file from a gro file is easy with grep, cut and awk. Make a gro file with trjconv, then process it with aforementioned tools. /Erik 21 sep 2007 kl. 17.33 skrev Naser, Md Abu: > Hi Gmx user, > > I have wondering whether it is possible to extract index numbers > for atoms from a particular > region in the box such as, if a box divided into 10 slices along z > and one wants to get all the atom's > index number of protein in 1st slice or 3rd, etc. > > With regards, > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy -fee -inf problem
Hi All User, I am getting free energy difference -inf. 1st I run a protein in water molecule and then I made a different topology file with deleting 4 disulfide bonds and accordingly the angles and diherdal angles. Then, I run -rerun for the both and and g_energy -fee, which giving me free energy difference -inf. Can anyone please point me out where I am making mistakes. With thanks in advance, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] atom index number
Hi Gmx user, I have wondering whether it is possible to extract index numbers for atoms from a particular region in the box such as, if a box divided into 10 slices along z and one wants to get all the atom's index number of protein in 1st slice or 3rd, etc. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_wham
hi Lanyuan, Thanks for your replay. I have tried the current(3.3.1) and 3.3 version g_wham. They both dont work. What do you mean by original? With best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 From: [EMAIL PROTECTED] on behalf of LuLanyuan Sent: Fri 14/09/2007 7:37 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_wham Hi, I don't remember whether the bug has been fixed for 3.3.*. Can any gromacs guy clarify that? Abu, have you tried the original g_wham first? If it really dosen't work, please shoot me an email. Then I can send you the correct file. Lanyuan Lu > Date: Fri, 14 Sep 2007 14:41:23 +0100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: [gmx-users] g_wham>> Hi,> Is there any way I can get corrected version of g_wham? I know form the discussion archive> that David Bostick has a copy of the corrected g_wham.> With regards,> Abu Naser> School Of Life Sciences> Heriot-Watt University> Edinburgh EH14 4AS> Email: [EMAIL PROTECTED]> Phone: +44(0)1314518265> Fax : +44(0) 131 451 3009 _ Windows Live Custom Domain,? https://domains.live.com/default.aspx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sorient segmenation fault
Hi All, I have been getting segmenation fault with current(3.3.1) version of g_sorient. Dose anybody know why? With best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_wham
Hi, Is there any way I can get corrected version of g_wham? I know form the discussion archive that David Bostick has a copy of the corrected g_wham. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rotational fit in XY plane only
> > I implemented an xy only fitting option for trjconv in the development > > branch. > > > > Berk. In reference to the above replay of Berk, I was trying to get into CVS to get a copy of it. When I click on the "instructions on how to access our CVS repository", it says not authorised to access. Can you help me to a get a copy with above changes? Best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] 2nd Virial coefficient and Hydrophobicmoment Calculation
Thanks David for your reply. Anybody has got the script for calculating 2nd virial coefficient or can you explain a bit more detail? Hydrophobic moment basically calculated as vector sum of hydrophobicities of amino acids and cross product of that sum with unit vector pointing from the alpha carbon atom of ith residue.(Zangi, et el, Biophysical Journal, 83: 112-124, 2002) With regards. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Fri 22/06/2007 8:40 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] 2nd Virial coefficient and Hydrophobicmoment Calculation Naser, Md Abu wrote: > Hi GMX user, > > Is there anyway I can calculate 2nd virial coefficient and hydrophobic > moment using gromacs? > I guess 2nd virial coefficient calculated somewhere in the gromacs. > > Thanking you, > 2nd virial: people use scripts that generate different orientations and distances and then compute it from there. Alternative would be to do gas sims at different T and measure the deviation from the ideal gas law. hydrophobic moment: don't know. what is that again? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 2nd Virial coefficient and Hydrophobic moment Calculation
Hi GMX user, Is there anyway I can calculate 2nd virial coefficient and hydrophobic moment using gromacs? I guess 2nd virial coefficient calculated somewhere in the gromacs. Thanking you, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem still lies regarding dssp
Hi Sangeeta, Your out dose not say that the programme is really running. Can you try with .trr and .tpr file and see you get something at the bottom of the output like: Reading frame 0 time0.000 Back Off! I just backed up ddQmCBhK to ./#ddQmCBhK.1# Reading frame 20 time 40.000 Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Mon 12/02/2007 9:55 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] problem still lies regarding dssp Dear Abu and Mark, You asked me, whether my computer is shared by many, it is not, I think the program was not hanged because while executing do_dssp -v as usual Gromacs output was given, ":-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) do_dssp (-: Option Filename Type Description -f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb -s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt. Index file -ssdump ssdump.dat Output, Opt. Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -sss string HEBT Secondary structures for structure count " I changed the permission of dsspcmbi and dsspcmbi.exe files , what else I should do? I mean execpt these two files what are the other files that need change of permission now these two files has read, write, and executable permission, Mark suggested me to call dssp "by hand", will you please explain in more detail?? In order to get taht particular coloured map what procedure should I adopt?? regards SANGEETA "Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To find out use: ls -l /directory/where/you/put/dssp If you see any restricton to file permission change it to chmod a+rx dssp Hope this will help. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Fri 09/02/2007 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] problem still lies regarding dssp Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not wor
RE: [gmx-users] problem still lies regarding dssp
Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To find out use: ls -l /directory/where/you/put/dssp If you see any restricton to file permission change it to chmod a+rx dssp Hope this will help. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Fri 09/02/2007 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] problem still lies regarding dssp Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all the other programs of Gromacs like pdb2gmx, editconf , genbox, grompp, mdrun etc are going on successfully, problem lies only in case of dssp, I was suggested by Mark to try dssp independently on a single snapshot extracted from the trajectory, I took the snapshot of the protein after 500ps with the command trjconv -f md.xtc -s md.tpr -o time_500ps.pdb -dump 500 (I think the command is correct, if not I earnestly request you to rectify my mistake), When I ran do_dssp on this single structure I waited for 3 days, but it did not finish and seems to be neverending, then I killed the program, In order to get that particular coloured plot of secondary structure vs time which method should I adopt? Seeking your help and thanks in advance. regards SANGEETA - Here's a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem regarding do_dssp
Try running with -v option. It might give you clue where is the problem. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Mon 05/02/2007 7:56 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] problem regarding do_dssp > > Dear All, > >I want to analyze the secondary structure of a protein after a 10ns > simulation run. Previously I faced difficulty in running dssp program,So > in > order to give a test run I ran the do_dssp program for 100ps > trajectory > only for a protein containing 130 residues.The program continued for more > than 4 days, yet it was not completed, Only it was giving the intermediate > files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I > do > not understand how long it will take or whether I am encountering any > problem , in the manual it is mentioned that the program is very slow, > But > I am not getting any idea whether the time it is taking is normal, or I > am > facing some problem. Try doing it on one structure in a trajectory by using trjconv appropriately. If it's not done in ten minutes on a machine under five years old, then you have a problem. Also try running dssp independently on a single snapshot extracted from your trajeotry and put into pdb format (by specifying .pdb suffix on output file for trjconv). If you can't do that, then the problem has nothing to do with gromacs. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] range checking error
Hi Giacomo, That is due to the bad starting structure. You might want to try with small time step and with no constrain. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Giacomo Bastianelli Sent: Tue 05/12/2006 10:16 AM To: Discussion list for GROMACS users Subject: [gmx-users] range checking error Dear Users, I am running MD of an homology model and even with a long energy minimization step a still get this error message: Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 1200 ] Please report this to the mailing list (gmx-users@gromacs.org) Thanks in advance, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] regarding comm_mode
Because in periodic or assymmetric system, the angular momentum is not conserved. You can find the explaination in computer simulation of liquids - Allen and Tldesley. Best wishes, Abu Naser From: [EMAIL PROTECTED]Sent: Mon 14/08/2006 11:58 AMTo: gmx-users@gromacs.orgSubject: [gmx-users] regarding comm_mode Dear users, There is an option in .mdp named comm_mode, which deals with the translation and rotation of the molecule being simulated. I want to know how and why the translation and rotation happens during the simulation and their significance. Can any one suggest me any reading material where in I can find how the dynamics is performed internally. thanks in advance regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] comm-mode = Angular
Hi Tsjerk, Thanks for the link. I have been wondering how to select roto-translation option. Is it in the mdp file? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 From: Tsjerk WassenaarSent: Wed 26/04/2006 12:05 PMTo: Discussion list for GROMACS usersSubject: Re: [gmx-users] comm-mode = Angular Hi Abu,In fact, I have it implemented in two versions (3.1.4 and 3.2.1), but haven't contributed it to the official code yet. At this point I don't have the time either :S However, you can download my versions at http://md.chem.rug.nl/~tsjerk/GMX/Cheers,Tsjerk On 4/26/06, Naser, Md Abu <[EMAIL PROTECTED]> wrote: Hi Tsjerk, I have been wondering whether Andrea Amadei and coworkers' method ( J. Chem. Phys. 112(1) pp. 9-23) has been implemented in Gromacs yet. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 From: David van der SpoelSent: Tue 25/04/2006 7:32 PMTo: Discussion list for GROMACS usersSubject: Re: [gmx-users] comm-mode = Angular Naser, Md Abu wrote:> Hi All,> > Dose anyone know any literature regarding comm-mode = Angular option?it just sets the overall angular momentum to zero.> With regards, > Abu Naser> > School Of Life Sciences> Heriot-Watt University> Edinburgh EH14 4AS> Email: [EMAIL PROTECTED] [EMAIL PROTECTED]>> Phone: +44(0)1314518265> Fax : +44(0) 131 451 3009> > > > > > > > > ___> gmx-users mailing list gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED].> Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se/___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] comm-mode = Angular
Hi Tsjerk, I have been wondering whether Andrea Amadei and coworkers' method ( J. Chem. Phys. 112(1) pp. 9-23) has been implemented in Gromacs yet. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 From: David van der SpoelSent: Tue 25/04/2006 7:32 PMTo: Discussion list for GROMACS usersSubject: Re: [gmx-users] comm-mode = Angular Naser, Md Abu wrote: > Hi All, > > Dose anyone know any literature regarding comm-mode = Angular option? it just sets the overall angular momentum to zero. > With regards, > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] comm-mode = Angular
Hi All, Dose anyone know any literature regarding comm-mode = Angular option? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] distance measurement
Title: RE: [gmx-users] distance measurement Hi Tsjerk, Thanks for your response. I mean edge of decane-water interface. I have a protein solvated in water and I want to measure distance between the interface and protein over time. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Tsjerk Wassenaar Sent: Thu 30/03/2006 7:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] distance measurement Hi Abu, What edge? There are no edges when using periodic boundary conditions. Is there any particular reason why you would need such a measurement? If you want the "distance to the wall", you will need to calculate the minimal distance between periodic images (g_mindist -pi) and take half of that. You could ofcourse take the maximal z-coordinate and subtract it from the third number of the last line of the .gro file (which gives the z component of the third box vector). Cheers, Tsjerk On 3/30/06, Naser, Md Abu <[EMAIL PROTECTED]> wrote: > > Hi All, > > Is there anyway I can measure distance between protein and edge of a box > in z direction? > > Regards, > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] distance measurement
Title: distance measurement Hi All, Is there anyway I can measure distance between protein and edge of a box in z direction? Regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Decabe density
Title: Decabe density Hi All User, I have made a decane box of roughly about 730gm/liter but when I allow vaccuume or put water for making an interface, it changes its density to roughly about 800gm/ liter or more on 2ns run. Is there anyone knows why this is happening? Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
