[gmx-users] g_rotacf
Dear All I have what might be a simple question. For g_rotacf, what is the equation used in the calculation of the rotational correlation function? is there any basic reference one could give me for the same? Also, for the rotational correlation function, is the decay something as simple as the autocorrelation of the angle wrt time? Thanks for your time Regards Rama __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] g_rdf
Dear Dr Spoel Thanks for the prompt reply. Yes I did shuffle the trajectories. I shall try to recompute after deshuffling the trajectories. Thanks again, Sincerely Regards RamaDavid van der Spoel <[EMAIL PROTECTED]> wrote: Rama Gullapalli wrote:> Hi GMX ers,> I posted this question earlier, but did not receive a reply. Hope to get > an answer this time around.> > I was wondering what could be the origin of a spike at close distances > when I compute the RDF of N-P atoms in a lipid bilayer system (<0.25 > nm) I tried using -cut option and also increasing the nrexcl to 5 in the > N and P atoms ( to avoid intramolecular contributions?)> And yet, I still get that spike.maybe your index file is incorrect, or the trajectory does not match the tpr (did you use shuffling?)> Any insight would be very helpful> Thanks> Rama> > > Everyone is raving about the all-new Yahoo! Mail. > > > > > > > ___> 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, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing listgmx-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 Sponsored LinkMortgage rates near historic lows: $150,000 loan as low as $579/mo. Intro-*Terms___ 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] g_rdf
Hi GMX ers, I posted this question earlier, but did not receive a reply. Hope to get an answer this time around.I was wondering what could be the origin of a spike at close distances when I compute the RDF of N-P atoms in a lipid bilayer system (<0.25 nm) I tried using -cut option and also increasing the nrexcl to 5 in the N and P atoms ( to avoid intramolecular contributions?) And yet, I still get that spike. Any insight would be very helpful Thanks Rama Everyone is raving about the all-new Yahoo! Mail.___ 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] g_rdf again
Dear All I am running a simulation of a DPPC bilayer. I am trying to compute the INTER molecular RDF s of the P-P atoms, N-P atoms and N-N atoms in the head of the bilayer. I have 2 questions, 1) When I compute RDF using g_rdf, instead of a getting a smoothly decaying curve at close distances (<0.3 nm) I get a spike (at around 0.22 nm). Is this due to INTRAmolecular RDF contribution? 2) If so, I probably need to increase the nexcl using a new tpr file right? What I am wondering is, how much do I need to set the nexcl for a DPPC molecule and what is the basis for it?Thanks a lotRama Want to start your own business? Learn how on Yahoo! Small Business. ___ 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] g_rdf again
Dear All I am running a simulation of a DPPC bilayer. I am trying to compute the INTER molecular RDF s of the P-P atoms, N-P atoms and N-N atoms in the head of the bilayer. I have 2 questions,1) When I compute RDF using g_rdf, instead of a getting a smoothly decaying curve at close distances (<0.3 nm) I get a spike (at around 0.22 nm). Is this due to INTRAmolecular RDF contribution? 2) If so, I probably need to increase the nexcl using a new tpr file right? What I am wondering is, how much do I need to set the nexcl for a DPPC molecule and what is the basis for it?Thanks a lot Rama Want to start your own business? Learn how on Yahoo! Small Business. ___ 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] g_rotacf again
Hello everybody.I have question regarding g_rotacfIf I wanted to compute the rotational correlation function of a linear vector which is between the "centers of masses" of two groups of atoms in an individual molecule (Instead of two atoms), how do I go about it?Can I use g_rotacf to do it ?Thanks in advanceRama Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1¢/min.___ 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] g_rotacf
Dear Dr Spoel Sorry for the earlier hasty mail. I figured out how the -noaver option works. Thanks Sincerely Regards RamaRama Gullapalli <[EMAIL PROTECTED]> wrote: Dear Dr SpoelThank you for the reply. But I do not quite follow how -noaver does it. I want to compute the P-N vector of lipid molecules and average it over the 128 molecules in the bilayer.Do I make a group containing the numbers of the P and N molecules in a single group ( 256 atoms) and use g_rotacf with -noaver? Will that compute the rotational correlation of the individual P-N vectors of each lipid molecule and average it over 128 molecules?Thanks in advanceRegardsRamaDavid van der Spoel <[EMAIL PROTECTED]> wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote:>Hello everybody,> > I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others.> -noaver> I would imagine one could use a awk script to run g_rotacf to run a hundred times, but I am not sure how to go about it. If anyone can provide me with pointers on that it would be great> > Thanks in advance> Rama> > >->Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1¢/min.-- 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://xray.bmc.uu.se/~spoel___gmx-users mailing listgmx-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 Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1¢/min.___gmx-users mailing listgmx-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 Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1¢/min.___ 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] g_rotacf
Dear Dr SpoelThank you for the reply. But I do not quite follow how -noaver does it. I want to compute the P-N vector of lipid molecules and average it over the 128 molecules in the bilayer.Do I make a group containing the numbers of the P and N molecules in a single group ( 256 atoms) and use g_rotacf with -noaver? Will that compute the rotational correlation of the individual P-N vectors of each lipid molecule and average it over 128 molecules?Thanks in advanceRegardsRamaDavid van der Spoel <[EMAIL PROTECTED]> wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote:>Hello everybody,> > I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others.> -noaver> I would imagine one could use a awk script to run g_rotacf to run a hundred times, but I am not sure how to go about it. If anyone can provide me with pointers on that it would be great> > Thanks in advance> Rama> > >->Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1¢/min.-- 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://xray.bmc.uu.se/~spoel___gmx-users mailing listgmx-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 Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1¢/min.___ 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] g_rotacf
Hello everybody,I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others.I would imagine one could use a awk script to run g_rotacf to run a hundred times, but I am not sure how to go about it. If anyone can provide me with pointers on that it would be greatThanks in advance Rama Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1¢/min.___ 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] Position of a molecule in a bilayer
Dear GMX ers I would like to compute the position of a small molecule inside a lipid bilayer as a function of its position along the Z axis. Which GMX program is best suited for this? I tried using g_traj, but I got some weird results when i computed the COM position of a DPPC molecule. The COM position of DPPC was crossing the center of the lipid bilayer which is weird. Thanks Rama Brings words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail.___ 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
