Re: [gmx-users] g_dist error

2011-09-13 Thread Thomas Schlesier
in every line. since i never used the -dist option, the stuff above could be false, so short thing you can do is and look if atom 62618 is in residue 20230, and then the above should be right. greetings thomas Date: Tue, 13 Sep 2011 13:32:26 +0530 From: aiswarya pawar Subject: Re: [gmx-users

Re: [gmx-users] g_dist error

2011-09-13 Thread aiswarya pawar
Y,Z output which I don't want. >>> >>> >>> And other output which you do, but you have to use -o to get it. Read >>> g_dist -h. >>> >>> >>> And am not specifying an -o. >>> >>> >>> You need to spec

Re: [gmx-users] g_dist error

2011-09-13 Thread Mark Abraham
To: <mailto:aiswarya.pa...@gmail.com>; Discussion list for GROMACS users <mailto:gmx-users@gromacs.org> Reply-To:jalem...@vt.edu <mailto:jalem...@vt.edu> Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com <mailto:aiswarya.pa...@gmai

Re: [gmx-users] g_dist error

2011-09-12 Thread aiswarya pawar
a while ago, there is no value in measuring the distance between a protein >> phase and a water phase if they are in contact... >> >> Mark >> >> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for >> it! >> >>

Re: [gmx-users] g_dist error

2011-09-12 Thread Mark Abraham
GROMACS users <mailto:gmx-users@gromacs.org> Reply-To:jalem...@vt.edu <mailto:jalem...@vt.edu> Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com <mailto:aiswarya.pa...@gmail.com> wrote: Even if I specify an atom say 1277 atom number to find dist

Re: [gmx-users] g_dist error

2011-09-12 Thread aiswarya pawar
t; > Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for > it! > > -Original Message- > From: "Justin A. Lemkul" > Date: Mon, 12 Sep 2011 22:35:28 > To: ; Discussion list > for GROMACS users > Reply-To: jalem...@vt.edu

Re: [gmx-users] g_dist error

2011-09-12 Thread Mark Abraham
erry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: "Justin A. Lemkul" Date: Mon, 12 Sep 2011 22:35:28 To:; Discussion list for GROMACS users Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote:

Re: [gmx-users] g_dist error

2011-09-12 Thread aiswarya . pawar
kul" Date: Mon, 12 Sep 2011 22:35:28 To: ; Discussion list for GROMACS users Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote: > Even if I specify an atom say 1277 atom number to find distance against the > OW atoms. I get the same result

Re: [gmx-users] g_dist error

2011-09-12 Thread Justin A. Lemkul
1 Network. Go for it! -Original Message- From: "Justin A. Lemkul" Sender: gmx-users-boun...@gromacs.org Date: Mon, 12 Sep 2011 07:52:54 To: Discussion list for GROMACS users Reply-To: jalem...@vt.edu, Discussion list for GROMACS users Subject: Re: [gmx-users] g_dist err

Re: [gmx-users] g_dist error

2011-09-12 Thread aiswarya . pawar
obile, India's No. 1 Network. Go for it! -Original Message- From: "Justin A. Lemkul" Sender: gmx-users-boun...@gromacs.org Date: Mon, 12 Sep 2011 07:52:54 To: Discussion list for GROMACS users Reply-To: jalem...@vt.edu, Discussion list for GROMACS users Subject: Re

Re: [gmx-users] g_dist error

2011-09-12 Thread Justin A. Lemkul
aiswarya pawar wrote: hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. The printed distance indicates that there is a certain water molecule that is just over 2 hydrogen bonding lengths awa

Re: [gmx-users] g_dist error

2011-09-12 Thread Justin A. Lemkul
aiswarya pawar wrote: Hi Justin, Am using g_dist to find the distance between water and protein. for that i made a index file such as- a CA(protein atoms) a OW(water atoms) i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35 instead of getting the result for p

Re: [gmx-users] g_dist error

2011-09-12 Thread aiswarya pawar
hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul wrote: > > > aiswarya pawar wrote: > >> Hi Users, >> >> Am using g_dist to find the dista

Re: [gmx-users] g_dist error

2011-09-12 Thread aiswarya pawar
Hi Justin, Am using g_dist to find the distance between water and protein. for that i made a index file such as- a CA(protein atoms) a OW(water atoms) i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35 instead of getting the result for protein-SOL distance . my out

Re: [gmx-users] g_dist error

2011-09-12 Thread Justin A. Lemkul
aiswarya pawar wrote: Hi Users, Am using g_dist to find the distance between water and protein. but my output has the values of SOL-water distance. t: 1 136 SOL 2336 OW 0.772373 (nm) This is not a water-water distance, it is the output of the -dist option telling you that water molecu

[gmx-users] g_dist error

2011-09-12 Thread aiswarya pawar
Hi Users, Am using g_dist to find the distance between water and protein. but my output has the values of SOL-water distance. t: 1 136 SOL 2336 OW 0.772373 (nm) Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arch

Re: [gmx-users] g_dist error?

2010-05-10 Thread Justin A. Lemkul
Marc Charendoff wrote: Hello, I am in the middle of analyzing the distance between two atoms of a MD trajectory when I ran into the following error thus stopping at 3 ns of a 4 ns trajectory. What could be the issue? Select a group: 18 Selected 18: 'a_1899' Select a group: 19 Selecte

[gmx-users] g_dist error?

2010-05-10 Thread Marc Charendoff
Hello, I am in the middle of analyzing the distance between two atoms of a MD trajectory when I ran into the following error thus stopping at 3 ns of a 4 ns trajectory. What could be the issue? Select a group: 18 Selected 18: 'a_1899' Select a group: 19 Selected 19: 'a_2498' trn version: