Dear Justin and all, In my results, that are not only 8 micelles but there are 2 aggregated micelles and some free monomers that made up total of 8. Then the graph also showed 8 number of clusters. that is what I am wonder is it monomer also counted? thanks for any comments.
QIU YI HUAN A beginner of Gromacs user. --- On Fri, 11/28/08, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > From: [EMAIL PROTECTED] <[EMAIL PROTECTED]> > Subject: gmx-users Digest, Vol 55, Issue 150 > To: [email protected] > Date: Friday, November 28, 2008, 11:21 PM > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/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 gmx-users digest..." > > > Today's Topics: > > 1. Re: Analyzing a trajectory split over multiple files > (TJ Piggot) > 2. Re: Fatal error with grompp(with detail process) > (Justin A. Lemkul) > 3. Re: Re: Re: defination of cluster (Justin A. Lemkul) > 4. RE: Box vector shifts number in x and y/z dimension > (Berk Hess) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 28 Nov 2008 11:47:55 +0000 > From: TJ Piggot <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Analyzing a trajectory split over > multiple > files > To: Discussion list for GROMACS users > <[email protected]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=iso-8859-1; format=flowed > > Just as a note most analysis tools have a -noxvgr option to > output the > results without any of the formatting information for > grace. > > Also I still think the easiest way to solve your problem is > to just > initially use trjcat to concatenate your trajectory, then > run the analysis > on this. > > Tom > > --On Friday, November 28, 2008 05:06:31 +0530 Suman > Chakrabarty > <[EMAIL PROTECTED]> wrote: > > > On Fri, Nov 28, 2008 at 4:24 AM, Nicolas > <[EMAIL PROTECTED]> wrote: > >> Suman Chakrabarty a écrit : > >>> It would have been much easier if there was > some way to concatenate > >>> the multiple .xvg files easily. Also, the > analysis programs should be > >>> able to export the output data in raw 2 (or > more) column format > >>> without all the formatting statements as an > option. > >>> > >> > >> Actually, there is: > >> > >> grep -v "^#" *.xvg > concatenate.xvg > >> > >> The -v "^#" will skip all the comment > lines of your xvg files. Of course, > >> this assumes that your xvg files are correctly > named, i.e. file01.xvg, > >> file02.xvg, etc. With a short shell script, you > can easily re-add the > >> comments at the beginning of your concatenate > file, renumber the frames > >> correctly, etc. It is more convenient to write a > Python or a Perl script > >> to do this kind of stuff, though. > >> > >> Nicolas > > > > > > > > Thank you very much! I always knew there must be > something smart to be > > done. I should now delve into the nitty-gritty of > scripting. grep > > seems to be a particularly useful tool! :) > > > > > > Regards, > > Suman. > > > > ---------------------- > TJ Piggot > [EMAIL PROTECTED] > University of Bristol, UK. > > > > ------------------------------ > > Message: 2 > Date: Fri, 28 Nov 2008 07:25:28 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Fatal error with grompp(with > detail process) > To: Discussion list for GROMACS users > <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Jenny Hsu wrote: > > Hi all: > > I have a problem with grompp > > I want to making "POPC+protein" file > > and I search the archieve and follow the process > > 1.run pdb2gmx for protein only > > 2.add below parameters into my topology file > > #include "ffG53a6.itp" > > #include "lipid.itp" > > #include "popc.itp" > > 3.adjust the [ molecules ] section to list the number > and type of my > > components > > 4.run editconf and genbox > > 5.run grompp and it shows > > Fatal error: > > Atomtype CA not found > > We just had a discussion about this: > > http://www.gromacs.org/pipermail/gmx-users/2008-November/038282.html > > You can copy the relevant portions of lipid.itp into the > appropriate sections in > ffG53a6nb.itp/ffG53a6bon.itp. Otherwise, including the > files as you have will > not work. > > -Justin > > > > > *Below is all information it shows* > > *Can someone help me to solve this problem?* > > *I am appreciate with that.* > > *Thaks.* > > :-) G R O M A C S (-: > > Getting the Right Output Means no Artefacts in > Calculating Stuff > > :-) VERSION 4.0 (-: > > Written by David van der Spoel, Erik Lindahl, > Berk Hess, and others. > > Copyright (c) 1991-2000, University of > Groningen, The Netherlands. > > Copyright (c) 2001-2008, The GROMACS > development team, > > check out http://www.gromacs.org > <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. > > :-) grompp (-: > > Option Filename Type Description > > > ------------------------------------------------------------ > > -f em.mdp Input, Opt! grompp input file > with MD parameters > > -po mdout.mdp Output grompp input file > with MD parameters > > -c 1UEO-nowater_water.gro Input Structure > file: gro g96 pdb > > tpr tpb > > tpa > > -r conf.gro Input, Opt. Structure file: gro > g96 pdb tpr tpb tpa > > -rb conf.gro Input, Opt. Structure file: gro > g96 pdb tpr tpb tpa > > -n index.ndx Input, Opt. Index file > > -p 1UEO-nowater.top Input Topology file > > -pp processed.top Output, Opt. Topology file > > -o 1UEO-nowater_em.tpr Output Run input file: > tpr tpb tpa > > -t traj.trr Input, Opt. Full precision > trajectory: trr trj cpt > > -e ener.edr Input, Opt. Energy file: edr ene > > Option Type Value Description > > ------------------------------------------------------ > > -[no]h bool no Print help info and quit > > -nice int 0 Set the nicelevel > > -[no]v bool yes Be loud and noisy > > -time real -1 Take frame at or first > after this time. > > -[no]rmvsbds bool yes Remove constant bonded > interactions with virtual > > sites > > -maxwarn int 0 Number of allowed warnings > during input > > processing > > -[no]zero bool no Set parameters for bonded > interactions without > > defaults to zero instead > of generating an error > > -[no]renum bool yes Renumber atomtypes and > minimize number of > > atomtypes > > Ignoring obsolete mdp entry 'title' > > Ignoring obsolete mdp entry 'cpp' > > Back Off! I just backed up mdout.mdp to > ./#mdout.mdp.2# > > checking input for internal consistency... > > processing topology... > > Opening library file > /usr/local/md/share/gromacs/top/ffG53a6.itp > > Opening library file > /usr/local/md/share/gromacs/top/ffG53a6nb.itp > > Opening library file > /usr/local/md/share/gromacs/top/ffG53a6bon.itp > > Opening library file > /usr/local/md/share/gromacs/top/ff_dum.itp > > WARNING 1 [file lipid.itp, line 14]: > > Overriding atomtype LO > > WARNING 2 [file lipid.itp, line 15]: > > Overriding atomtype LOM > > WARNING 3 [file lipid.itp, line 16]: > > Overriding atomtype LNL > > WARNING 4 [file lipid.itp, line 17]: > > Overriding atomtype LC > > WARNING 5 [file lipid.itp, line 18]: > > Overriding atomtype LH1 > > WARNING 6 [file lipid.itp, line 19]: > > Overriding atomtype LH2 > > WARNING 7 [file lipid.itp, line 20]: > > Overriding atomtype LP > > WARNING 8 [file lipid.itp, line 21]: > > Overriding atomtype LOS > > WARNING 9 [file lipid.itp, line 22]: > > Overriding atomtype LP2 > > WARNING 10 [file lipid.itp, line 23]: > > Overriding atomtype LP3 > > WARNING 11 [file lipid.itp, line 24]: > > Overriding atomtype LC3 > > WARNING 12 [file lipid.itp, line 25]: > > Overriding atomtype LC2 > > WARNING 13 [file lipid.itp, line 108]: > > Overriding non-bonded parameters, > > old: 0.00238804 3.38411e-06 new > > LNL C 1 2.387718e-03 2.389594e-06 > > > ------------------------------------------------------- > > Program grompp, VERSION 4.0 > > Source code file: toppush.c, line: 793 > > Fatal error: > > Atomtype CA not found > > > > > > -- > > Jenny Hsu, Biotechnology Dept., > > Ming Chuan University, Taiwan, R.O.C > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Fri, 28 Nov 2008 07:29:12 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Re: Re: defination of cluster > To: [EMAIL PROTECTED], Discussion list for GROMACS > users > <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Q. Y. HUAN wrote: > > Dear Mark and all, > > Yes, I read it before I start. It states that the > program computes the size distributions of molecular/atomic > clusters in gas phase. Is it means that even a single > molecule, it is also defined as a cluster? > > Thanks for the help. > > > > > > In my mind, that would make no sense. Also, think about > your results that you > told us about - 8 micelles, and 8 aggregates detected. Do > you think that the > monomers are being considered? > > -Justin > > > > > > > QIU YI HUAN > > DEPARTMENT OF CHEMISTRY, > > FACULTY OF SCIENCE, > > UNIVERSITY PUTRA MALAYSIA, > > MALAYSIA. > > > > > > --- On Fri, 11/28/08, [EMAIL PROTECTED] > <[EMAIL PROTECTED]> wrote: > > > >> From: [EMAIL PROTECTED] > <[EMAIL PROTECTED]> > >> Subject: gmx-users Digest, Vol 55, Issue 147 > >> To: [email protected] > >> Date: Friday, November 28, 2008, 3:59 PM > >> Send gmx-users mailing list submissions to > >> [email protected] > >> > >> To subscribe or unsubscribe via the World Wide > Web, visit > >> http://www.gromacs.org/mailman/listinfo/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 gmx-users > digest..." > >> > >> > >> Today's Topics: > >> > >> 1. Re: defination of cluster (Mark Abraham) > >> 2. Box vector shifts number in x and y/z > dimension > >> (xuji) > >> 3. How to calculate virial in gromacs-4.0? > (xuji) > >> 4. RE: PME-user for electrostatics (Berk Hess) > >> 5. Fatal error with grompp(with detail process) > (Jenny > >> Hsu) > >> > >> > >> > ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Fri, 28 Nov 2008 12:24:52 +1100 > >> From: Mark Abraham <[EMAIL PROTECTED]> > >> Subject: Re: [gmx-users] defination of cluster > >> To: Discussion list for GROMACS users > >> <[email protected]> > >> Message-ID: <[EMAIL PROTECTED]> > >> Content-Type: text/plain; charset=ISO-8859-1; > format=flowed > >> > >> Q. Y. HUAN wrote: > >>> Dear all, > >>> > >>> I did the g_clustsize to get the number of > cluster > >> graph for my system. At the end of the simulation, > the total > >> number of cluster shown in the graph of my system > was 8. > >> Then I had a view in the trjectory and I found > that there > >> were total of 8 aggregated micelles and some free > monomer > >> (even it is a single molecule) which is same with > the result > >> shown in the graph. > >>> ie 8 in the graph, 8 in the trajectory > >>> > >>> > >>> My question is, how Gromacs define the > defination of > >> cluster? In my case, is it a free monomer (single > free > >> molecule) is also counted? > >> > >> Did you start by reading g_clustsize -h? > >> > >> Mark > >> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Fri, 28 Nov 2008 09:41:31 +0800 > >> From: "xuji"<[EMAIL PROTECTED]> > >> Subject: [gmx-users] Box vector shifts number in x > and y/z > >> dimension > >> To: "[email protected]" > >> <[email protected]> > >> Message-ID: > >> <[EMAIL PROTECTED]> > >> Content-Type: > text/plain; charset="gb2312" > >> > >> Hi all: > >> > >> In gromacs all atoms are in the rectangular or > triclinic > >> unit-cell, > >> and in the codes using shifts with periodic > boundary > >> condition. > >> But why are there only single box vector shifts > required in > >> y and z dimensions > >> but 2 in x dimension ? > >> > >> Thanks for any help in advance! > >> > >> > 　　　　　　　　xuji > >> > [EMAIL PROTECTED] > >> > 　　　　　　　　　　2008-11-28 > >> > >> > >> ------------------------------ > >> > >> Message: 3 > >> Date: Fri, 28 Nov 2008 15:32:55 +0800 > >> From: "xuji"<[EMAIL PROTECTED]> > >> Subject: [gmx-users] How to calculate virial in > >> gromacs-4.0? > >> To: "[email protected]" > >> <[email protected]> > >> Message-ID: > >> <[EMAIL PROTECTED]> > >> Content-Type: > text/plain; charset="gb2312" > >> > >> Hi all > >> > >> I want to do pressure coupling in my own program. > >> So These days I read associated codes in > Gromacs_4.0 and I > >> find that it > >> must sum the virial first. In Gromacs-3.3.3 you > use the > >> intramolecular shift(graph) > >> to sum the virial of the covalent bonds, but in > Gromacs-4.0 > >> the graph variable seems to be NULL > >> when run the mdrun with domain decomposition. Is > it the > >> true? > >> And if it's true how do you sum the virial > with the > >> periodic boundary condition > >> in Gromacs_4.0 with domain decomposition? Can > someone > >> explain the way of summing > >> virial in Gromacs_4.0 in detail? Or can you > recommend some > >> resoures about summing the virial with > >> the periodic boundary condition? > >> > >> Appreciate any help in advance! > >> > >> Best > >> wishes! > >> > >> > >> > 　　　　　　　　xuji > >> > [EMAIL PROTECTED] > >> > 　　　　　　　　　　2008-11-28 > >> > >> ------------------------------ > >> > >> Message: 4 > >> Date: Fri, 28 Nov 2008 08:56:16 +0100 > >> From: Berk Hess <[EMAIL PROTECTED]> > >> Subject: RE: [gmx-users] PME-user for > electrostatics > >> To: Discussion list for GROMACS users > >> <[email protected]> > >> Message-ID: > >> > <[EMAIL PROTECTED]> > >> Content-Type: text/plain; > charset="iso-8859-1" > >> > >> > >> Hi, > >> > >> PME splits the calculation in a Mesh part and a > direct > >> space part, > >> which is normally 1/r minus the mesh part. Note > that the > >> mesh part > >> also contributes below the cut-off. > >> If you want something else than 1/r at short range > >> (you always have 1/r beyond the cut-off) > >> than you can just give the short-range potential > you want, > >> mdrun takes care that it subtracts the short range > >> contribution of the mesh part. > >> > >> Berk > >> > >>> Date: Thu, 27 Nov 2008 13:37:36 -0800 > >>> From: [EMAIL PROTECTED] > >>> To: [email protected] > >>> Subject: [gmx-users] PME-user for > electrostatics > >>> > >>> hi, > >>> > >>> i want to use a different function than the > Coulomb to > >> calculate the electrostatics > >>> between charged ions. So i am thinking to user > the > >> PME-user option for the electrostatics. > >>> The manual says for the PME-user > option"The PME > >> mesh contribution is subtracted from the user > table by > >> mdrun". > >>> what that means? should i have to add the > >> short-range-potential (given by equation-4.33 in > the manual) > >>> in the user table, because that will be > subtracted > >> with the mdrun? > >>> please let me know, and thanks a lot for your > help > >>> > >>> > >>> > >>> > _______________________________________________ > >>> gmx-users mailing list > [email protected] > >>> > 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 > >> > >> > _________________________________________________________________ > >> Express yourself instantly with MSN Messenger! > Download > >> today it's FREE! > >> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: > >> > http://www.gromacs.org/pipermail/gmx-users/attachments/20081128/0f3a29db/attachment-0001.html > >> > >> ------------------------------ > >> > >> Message: 5 > >> Date: Fri, 28 Nov 2008 15:58:41 +0800 > >> From: "Jenny Hsu" > <[EMAIL PROTECTED]> > >> Subject: [gmx-users] Fatal error with grompp(with > detail > >> process) > >> To: "Discussion list for GROMACS users" > >> <[email protected]> > >> Message-ID: > >> > <[EMAIL PROTECTED]> > >> Content-Type: text/plain; > charset="iso-8859-1" > >> > >> Hi all: > >> I have a problem with grompp > >> I want to making "POPC+protein" file > >> and I search the archieve and follow the process > >> 1.run pdb2gmx for protein only > >> 2.add below parameters into my topology file > >> #include "ffG53a6.itp" > >> #include "lipid.itp" > >> #include "popc.itp" > >> 3.adjust the [ molecules ] section to list the > number and > >> type of my > >> components > >> 4.run editconf and genbox > >> 5.run grompp and it shows > >> Fatal error: > >> Atomtype CA not found > >> > >> *Below is all information it shows* > >> *Can someone help me to solve this problem?* > >> *I am appreciate with that.* > >> *Thaks.* > >> :-) G R O M A C S (-: > >> Getting the Right Output Means no > Artefacts in > >> Calculating Stuff > >> :-) VERSION 4.0 (-: > >> Written by David van der Spoel, Erik > Lindahl, Berk > >> Hess, and others. > >> Copyright (c) 1991-2000, University of > Groningen, > >> The Netherlands. > >> Copyright (c) 2001-2008, 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. > >> :-) grompp (-: > >> Option Filename Type Description > >> > ------------------------------------------------------------ > >> -f em.mdp Input, Opt! grompp input > file with MD > >> parameters > >> -po mdout.mdp Output grompp input file > with MD > >> parameters > >> -c 1UEO-nowater_water.gro Input > Structure file: > >> gro g96 pdb tpr > >> tpb > >> tpa > >> -r conf.gro Input, Opt. Structure file: > gro g96 > >> pdb tpr tpb tpa > >> -rb conf.gro Input, Opt. Structure file: > gro g96 > >> pdb tpr tpb tpa > >> -n index.ndx Input, Opt. Index file > >> -p 1UEO-nowater.top Input Topology file > >> -pp processed.top Output, Opt. Topology file > >> -o 1UEO-nowater_em.tpr Output Run input > file: tpr > >> tpb tpa > >> -t traj.trr Input, Opt. Full precision > >> trajectory: trr trj cpt > >> -e ener.edr Input, Opt. Energy file: edr > ene > >> Option Type Value Description > >> > ------------------------------------------------------ > >> -[no]h bool no Print help info and > quit > >> -nice int 0 Set the nicelevel > >> -[no]v bool yes Be loud and noisy > >> -time real -1 Take frame at or first > after > >> this time. > >> -[no]rmvsbds bool yes Remove constant bonded > >> interactions with virtual > >> sites > >> -maxwarn int 0 Number of allowed > warnings > >> during input > >> processing > >> -[no]zero bool no Set parameters for > bonded > >> interactions without > >> defaults to zero > instead of > >> generating an error > >> -[no]renum bool yes Renumber atomtypes and > minimize > >> number of > >> atomtypes > >> Ignoring obsolete mdp entry 'title' > >> Ignoring obsolete mdp entry 'cpp' > >> Back Off! I just backed up mdout.mdp to > ./#mdout.mdp.2# > >> checking input for internal consistency... > >> processing topology... > >> Opening library file > >> /usr/local/md/share/gromacs/top/ffG53a6.itp > >> Opening library file > >> /usr/local/md/share/gromacs/top/ffG53a6nb.itp > >> Opening library file > >> /usr/local/md/share/gromacs/top/ffG53a6bon.itp > >> Opening library file > >> /usr/local/md/share/gromacs/top/ff_dum.itp > >> WARNING 1 [file lipid.itp, line 14]: > >> Overriding atomtype LO > >> WARNING 2 [file lipid.itp, line 15]: > >> Overriding atomtype LOM > >> WARNING 3 [file lipid.itp, line 16]: > >> Overriding atomtype LNL > >> WARNING 4 [file lipid.itp, line 17]: > >> Overriding atomtype LC > >> WARNING 5 [file lipid.itp, line 18]: > >> Overriding atomtype LH1 > >> WARNING 6 [file lipid.itp, line 19]: > >> Overriding atomtype LH2 > >> WARNING 7 [file lipid.itp, line 20]: > >> Overriding atomtype LP > >> WARNING 8 [file lipid.itp, line 21]: > >> Overriding atomtype LOS > >> WARNING 9 [file lipid.itp, line 22]: > >> Overriding atomtype LP2 > >> WARNING 10 [file lipid.itp, line 23]: > >> Overriding atomtype LP3 > >> WARNING 11 [file lipid.itp, line 24]: > >> Overriding atomtype LC3 > >> WARNING 12 [file lipid.itp, line 25]: > >> Overriding atomtype LC2 > >> WARNING 13 [file lipid.itp, line 108]: > >> Overriding non-bonded parameters, > >> old: 0.00238804 3.38411e-06 new > >> LNL C 1 2.387718e-03 2.389594e-06 > >> > ------------------------------------------------------- > >> Program grompp, VERSION 4.0 > >> Source code file: toppush.c, line: 793 > >> Fatal error: > >> Atomtype CA not found > >> > >> > >> -- > >> Jenny Hsu, Biotechnology Dept., > >> Ming Chuan University, Taiwan, R.O.C > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: > >> > http://www.gromacs.org/pipermail/gmx-users/attachments/20081128/7cbaf26c/attachment.html > >> > >> ------------------------------ > >> > >> _______________________________________________ > >> gmx-users mailing list > >> [email protected] > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > http://www.gromacs.org/search > >> before posting! > >> > >> End of gmx-users Digest, Vol 55, Issue 147 > >> ****************************************** > > > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Fri, 28 Nov 2008 16:20:57 +0100 > From: Berk Hess <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] Box vector shifts number in x and > y/z > dimension > To: Discussion list for GROMACS users > <[email protected]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-2022-jp" > > > Hi, > > The b and c box vectors can be such that they both have as > x component > half the vector a x-length. Thus together they can cause a > shift of 1 full > x length and thus you might need 2 shifts along x. > > Berk > > > Date: Fri, 28 Nov 2008 09:41:31 +0800 > > From: [EMAIL PROTECTED] > > To: [email protected] > > Subject: [gmx-users] Box vector shifts number in x and > y/z dimension > > > > Hi all: > > > > In gromacs all atoms are in the rectangular or > triclinic unit-cell, > > and in the codes using shifts with periodic boundary > condition. > > But why are there only single box vector shifts > required in y and z dimensions > > but 2 in x dimension ? > > > > Thanks for any help in advance! > > > > $B!!!!!!!!!!!!!!!!(Bxuji > > $B!!!!!!!!!!!!!!!!([EMAIL PROTECTED] > > $B!!!!!!!!!!!!!!!!!!!!(B2008-11-28 > > > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download > today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20081128/b82adbe7/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > > End of gmx-users Digest, Vol 55, Issue 150 > ****************************************** _______________________________________________ gmx-users mailing list [email protected] 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
