[gmx-users] micelle clustering

2011-12-24 Thread mohammad agha
Dear GROMACS users I want to analysis of 2 micelles that are created in one simulation, when I view output of trajectory by vmd or ngmx: ngmx -f md.trr -s md.tpr has been created 2 micelles, then I try to micelle clustering by: 1. trjconv -f md.xtc -o a_cluster.gro -e 0.001 -pbc

Re: [gmx-users] micelle clustering

2011-12-24 Thread Mark Abraham
On 12/24/2011 8:01 PM, mohammad agha wrote: Dear GROMACS users I want to analysis of 2 micelles that are created in one simulation, when I view output of trajectory by vmd or ngmx: ngmx -f md.trr -s md.tpr has been created 2 micelles, then I try to micelle clustering by: 1. |trjconv -f

Re: [gmx-users] micelle clustering

2011-12-24 Thread mohammad agha
Thank you very much. Best Regards Sara From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 24, 2011 1:48 PM Subject: Re: [gmx-users] micelle clustering On 12/24/2011 8:01 PM

Re: [gmx-users] micelle clustering

2011-07-01 Thread Mark Abraham
On 1/07/2011 3:35 PM, sulatha M. S wrote: Hi Tsjerk, I installed gromacs myself. I put the modified gmx_trjconv.c code in the /src/tools subdirectory where the source code is located and tried the command make trjconv But it gives me a series of error messages, as given below. They're all

Re: [gmx-users] micelle clustering

2011-07-01 Thread sulatha M. S
Thanks Mark, I will do the analysis in 4.5.4. Hope while doing the micelle clustering I will not get into a infinite loop as in 4.0.7. If I understand correctly, While using trjconv -pbc cluster, I should use -e 0.002 or the frames (-dump option) in the xtc file (generated after the micelles

Re: [gmx-users] micelle clustering

2011-07-01 Thread Tsjerk Wassenaar
Hi Sulatha, With my clustering algorithm there can be no infinite loop :) By the way, sorry for the error messages you ran into with compiling 4.0.7. It had escaped me that these changes were made after that version. Cheers, Tsjerk On Fri, Jul 1, 2011 at 8:29 AM, sulatha M. S

[gmx-users] micelle clustering

2011-06-30 Thread sulatha M. S
Hi all, I have simulated a system of randomly dispersed surfactants in water using gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns. I am using a time step of 0.002 fs with xtc files written every 500 steps. For analyzing the micellar properties, I tried the commands

Re: [gmx-users] micelle clustering

2011-06-30 Thread gregory megariotis
Dear Sulatha, You can try the command trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002 with GROMACS 4.5.4. Best regrds Grigoris --- Στις Πέμ., 30/06/11, ο/η sulatha M. S mssula...@gmail.com έγραψε: Από: sulatha M. S mssula...@gmail.com Θέμα: [gmx-users] micelle clustering Προς: Discussion

Re: [gmx-users] micelle clustering

2011-06-30 Thread Tsjerk Wassenaar
* έγραψε: Από: sulatha M. S mssula...@gmail.com Θέμα: [gmx-users] micelle clustering Προς: Discussion list for GROMACS users gmx-users@gromacs.org Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18 Hi all, I have simulated a system of randomly dispersed surfactants in water using gromacs (4.0.7

Re: [gmx-users] micelle clustering

2011-06-30 Thread sulatha M. S
Sulatha, You can try the command trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002with GROMACS 4.5.4. Best regrds Grigoris --- Στις *Πέμ., 30/06/11, ο/η sulatha M. S mssula...@gmail.com* έγραψε: Από: sulatha M. S mssula...@gmail.com Θέμα: [gmx-users] micelle clustering Προς: Discussion list