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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 of SOL
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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
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 of SOL-OW distance. Is it a bug cause
even after specifying one atom from a protein why
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 pawaraiswarya.pa...@gmail.com
Subject: Re: [gmx-users] g_dist error
To: Discussion list for GROMACS usersgmx-users
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
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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
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
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 jalem...@vt.edu wrote:
aiswarya pawar wrote:
Hi Users,
Am using g_dist to find the
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
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
gmx-users@gromacs.org
Subject: Re: [gmx-users] g_dist error
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
Subject: Re: [gmx-users] g_dist error
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
...@vt.edu
Date: Mon, 12 Sep 2011 22:35:28
To: aiswarya.pa...@gmail.com; Discussion list for GROMACS
usersgmx-users@gromacs.org
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
: Re: [gmx-users] g_dist error
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
...@vt.edu,
Discussion list for GROMACS users gmx-users@gromacs.org
gmx-users@gromacs.org
Subject: Re: [gmx-users] g_dist error
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
@gromacs.org 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 distance against the
OW atoms
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:
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
18 matches
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