Re: [gmx-users] different between g_hbond version

Dear Erik which version of g_hbond is correct so that i ll use that for my analysis E R Azhagiya singam From: Erik Marklund To: Discussion list for GROMACS users Cc: babu gokul Sent: Mon, 14 February, 2011 4:20:32 PM Subject: Re: [gmx-users] different

[gmx-users] different between g_hbond version

Dear all I have been using g_hbond of gromacs4.0.7 and 4.5.3 both gives me different results. is there any updates in the hbond tool E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www

[gmx-users] Molecular dynamics hydration site

Dear all "http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B94RW-4TYB1FX-K-1&_cdi=56421&_user=1245000&_pii=S0006349500765337&_coverDate=12/31/2000&_sk=%23TOC%2356421%232000%23999209993%23703217%23FLA%23display%23Volume_79,_Issue_6,_Pages_2783-3354_(December_2000)%23tagged%23Volume%23first%3

[gmx-users] GridCount

Dear all I would like to analysis the hydration site near the proteins the one done by the following paper "Biophysical Journal Volume 79 December 2000 2966–2974" I would like to do the analysis the trajectory like this. is this possible to do with GridCound tool if it is possible please

[gmx-users] water hydration map analysis help

Dear all I would like to analysis the hydration site near the proteins the one done by the following paper "Biophysical Journal Volume 79 December 2000 2966–2974" I would like to do the analysis the trajectory like this.is there any tool available in gromacs to do this kind of analysis

[gmx-users] hydration maps

Dear all I would like to analysis the hydration site near the proteins the one done by the following paper "Biophysical Journal Volume 79 December 2000 2966–2974" is there any tool available in gromacs to do this kind of analysis could anyone help me in this regard. what tool will be useful to

[gmx-users] About Zn paramter

Dear all I am including the parameter for the Zinc in the topology file all the bonded and nonbonded parameters have been included in the topology still it is not accepting the parameter the Zn atom move away from the coordination. Thanking you in advance E R Azhagiya singam -- gmx-users m

[gmx-users] reg. water mol. and its residence time

Dear friends I would like to get the water molecule residue no which is near a protein molecule active site and its residence time could anyone please help me in this regard Thanking you E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] intersting problem

dear all I want to calculate the how many water molecule are their with in 3.5 A of a particular atom. could anyone help me in this regard E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] g_sorient

Dear all when i try to run g_sorient with g_sorient -f prod_full.xtc -s prod.tpr -o ANALYSIS/sorie nt/sori.xvg -no ANALYSIS/sorient/snor.xvg -ro ANALYSIS/sorient/sord.xvg I am getting a segmentation fault what would be the problem could anyone help in in this regard E R Azhagiya singam --

[gmx-users] about do_dssp

dear all I am analyzing a collagen dynamics i would like to analysis the collagen structure in and its parameter ? what is the difference between beta bridge and beta strand. thank you E R azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

[gmx-users] water mediated hydrogen bond

Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen medi

[gmx-users] water mediated hydrogen bond

Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen medi

[gmx-users] water Mediated Hydrogen Bond

Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen medi

[gmx-users] about H-Bonds g_hbond

Hi all I am getting an error in g_hbond such as  " Program g_hbond_d, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest."  Could anyone tell me how to solve this problem. thanks in advance E R Azhagiya singam Send free SMS to your Friends on M

[gmx-users] Random Accelerator Molecular Dynamics

Hi all I would like to know whether Random Accelerator Molecular Dynamics is available in Gromacs as it is available in AMBER. E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gro

[gmx-users] git installation error

 I tried to install git version of Gromacs but when i make the file its shows the following error "cc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -m

[gmx-users] about Git in Gromacs

Hi all I am new to git. when i tried to get the git version of gromacs by uisng the command "git clone git://git.gromacs.org/gromacs.git" in Cygwin i got an error saying "Initialized empty Git repository in /home/admin/gromacs/.git/ fatal: Unable to look up git.gromacs.org (Unknown host)

[gmx-users] About Git version of Gromacs

Hi all I am new to git. when i tried to get the git version of gromacs by uisng the command "git clone git://git.gromacs.org/gromacs.git" in Cygwin i got an error saying "Initialized empty Git repository in /home/admin/gromacs/.git/ fatal: Unable to look up git.gromacs.org (Unknown host) fet

[gmx-users] (no subject)

Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue.  I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you

[gmx-users] About Zinc coordination

Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue.  I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R

[gmx-users] About Zinc coordination

Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue.  I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you