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.
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: gmx-users@gromacs.org > Date: Friday, November 28, 2008, 3:59 PM > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > 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 > <gmx-users@gromacs.org> > 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: "gmx-users@gromacs.org" > <gmx-users@gromacs.org> > 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: "gmx-users@gromacs.org" > <gmx-users@gromacs.org> > 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 > <gmx-users@gromacs.org> > 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: gmx-users@gromacs.org > > 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 gmx-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 > > _________________________________________________________________ > 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" > <gmx-users@gromacs.org> > 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 > gmx-users@gromacs.org > 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 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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