Thanks for the reply. I used following command to extract first frame that has all the surfectants ( as suggested by first step for characterizing micelle clustering). trjconv -f a.xtc -o a_cluster.gro -dump 0 -pbc cluster Here is the output I got:COM: 0.000 0.000 19.999 iter = 19526 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19527 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19528 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19529 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19530 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19531 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19532 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19533 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19534 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19535 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19536 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19537 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19538 Isq = 12671033.000 looks like lsq is only fluctuating between two numbers and the program is in an infinte loop. Jagannath --- On Wed, 7/7/10, Mark Abraham <mark.abra...@anu.edu.au> wrote:
From: Mark Abraham <mark.abra...@anu.edu.au> Subject: Re: [gmx-users] problem with trjconv -pbc cluster To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Wednesday, 7 July, 2010, 12:20 PM ----- Original Message ----- From: jagannath mondal <jmondal2...@yahoo.co.in> Date: Wednesday, July 7, 2010 16:36 Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org > Hi, I had a system of surfectants which are started with an initial > configuration where all of them are well dispersed. Visual study of > trajectory shows they start aggregating and finally form two discrete > micelles. > To quantify this micelle clusterization, I tried to use the > suggestions present in the gromacs documentations:> > http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering> > i.e > > use trjconv -pbc cluster to obtain a single frame that has all of > the lipids in the unit cell. This must be the first frame of your > trajectory. A similar frame from some previous timepoint will not work.> > use grompp to make a new tpr file based on the frame that was output from the > step above.> use trjconv -pbc nojump to produce the desired trajectory using > the newly produced tpr file.> trjconv -f a.xtc -o a_cluster.gro -e 0.001 > -pbc cluster> grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr> trjconv -f > a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump > But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is > going through an infinite loop and is not stopping for convergence. So what command did you give, what output did you get, and does the command make sense with respect to your trajectory contents? Mark > > I am using gromacs 4.0.7> > Any help will be appreciated.> > Jagannath> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -----Inline Attachment Follows----- -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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