Re: [gmx-users] micelle clustering

Thank you very much. Best Regards Sara From: Mark Abraham To: Discussion list for GROMACS users Sent: Saturday, December 24, 2011 1:48 PM Subject: Re: [gmx-users] micelle clustering On 12/24/2011 8:01 PM, mohammad agha wrote: Dear GROMACS users > &

Re: [gmx-users] micelle clustering

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 md.xt

[gmx-users] micelle clustering

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 cluster

Re: [gmx-users] micelle clustering

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 wrote: > Thanks M

Re: [gmx-users] micelle clustering

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 are

Re: [gmx-users] micelle clustering

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 m

Re: [gmx-users] micelle clustering

:1611: warning: passing argument 1 of 'read_next_frame' makes integer from pointer without a cast gmx_trjconv.c:1611: warning: passing argument 2 of 'read_next_frame' from incompatible pointer type gmx_trjconv.c:1611: error: too many arguments to function 'read_next_frame&#x

Re: [gmx-users] micelle clustering

1, ο/η sulatha M. S * έγραψε: > > > Από: sulatha M. S > Θέμα: [gmx-users] micelle clustering > Προς: "Discussion list for GROMACS users" > Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18 > > > Hi all, > > I have simulated a system of randomly dispersed surfacta

Re: [gmx-users] micelle clustering

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 έγραψε: Από: sulatha M. S Θέμα: [gmx-users] micelle clustering Προς: "Discussion list for GROMACS users"

[gmx-users] micelle clustering

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 gi