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:
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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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
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
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
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
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
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
obile, India's No. 1 Network. Go for it!
-Original Message-
From: "Justin A. Lemkul"
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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
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
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
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:
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
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
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!
>>
>>
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
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
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
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