Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist, the
output is printed on the terminal, but I want them into a file as separately.
May I ask you to help me, Please?
Thank you in advance
Best Regards
Sara
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gmx-users mailing listgmx-users@
Dear Justin,
Thank you very much from your answer.
May I ask you to help me more, Please?
I work with UBUNTU, I don't know how should I do it!
Best Regards
Sara
On 5/10/13 11:27 AM, mohammad agha wrote:
> Dear GROMACS Specialists,
> I have one problem with g_dist. When I use g_dist along wi
Dear Justin,
Thank you very much from your help.
Best Regards
Sara
On 5/10/13 11:27 AM, mohammad agha wrote:
> Dear GROMACS Specialists,
> I have one problem with g_dist. When I use g_dist along with option -dist,
> the output is printed on the terminal, but I want them into a file as
> sepa
Dear GROMACS Specialists,
I want to obtain number of instances the different atoms was found within a
spherical shell of width 0.02 nm at a distance r
from the micelle COM. For this, I use g_dist -dist, but when I select for
example 0.04, it also result all instances in 0-0.02, whereas I want on
Dear Gromacs specialists,
Can you help me about g_dist?
I have a micelle system, I want to obtain distance between center of mass of
micelle with the last of carbon bounded to head group in surfactant.
It should be near 2.2 but when I did "g_dist -f md.xtc -s md.tpr -b 15 -o
dist.xvg" an
Dear Prof.
Thank you very much from your response.
Yes, dist.xvg has four column consists origin distance and distances in
direction x, y , z. So distance that I want according to result of g_analyze,
is 5.324286e-02 that isn't correct. I selected 2 groups, micelle and the last
carbon bounded
[gmx-users] g_dist
dina dusti wrote:
> Dear Prof.
>
> Thank you very much from your response.
> Yes, dist.xvg has four column consists origin distance and distances in
> direction x, y , z. So distance that I want according to result of g_analyze,
> is 5.324286e-02 that isn&
Dear Prof.
Thank you very much from your response.
I removed pbc and jump in my system, and when I see my system as visual in
ngmx, there is not pbc and jump and has been created one micelle and it remain
stable for long times.
I really don't know what should I do!
Best Regards
Dina
--
gmx-us
day, February 1, 2012 9:15 PM
Subject: Re: [gmx-users] g_dist
dina dusti wrote:
> Dear Prof.
>
> Thank you very much from your response.
> but I didn't select micelle headgroups and then terminal carbon atom but also
> I selected COM of micelle and for example head gro
Dear Prof.
Thank you very much from your response.
He answer me that I should use from g_gyration for radius of micelle, but what
should I do for hydrocarbon (dry) core or calculation of inner core of micelle
(i.e. the first of carbon on tail of surfactant with COM of micelle)?
Best Regards
Di
again.
Best Regards
Dina
From: Justin A. Lemkul
To: dina dusti ; Discussion list for GROMACS users
Sent: Thursday, February 2, 2012 12:08 AM
Subject: Re: [gmx-users] g_dist
dina dusti wrote:
> Dear Prof.
>
> Thank you very much from your respons
for GROMACS users
Sent: Thursday, February 2, 2012 2:42 PM
Subject: Re: [gmx-users] g_dist
dina dusti wrote:
> Dear Prof.
>
> Thank you very much from your response.
> OK, I use from g_gyrate for all of radius, but I still don't understand that
> what thing did they use i
ay, February 2, 2012 6:07 PM
Subject: Re: [gmx-users] g_dist
dina dusti wrote:
> Dear Prof.
>
> Thank you very much from your response.
> Yes, I contacted with one of them and she said me use g_dist, but I have
> problem with it.
>
Perhaps she could be more specific. O
Dear Prof.
Thank you very much from your help.
Best Regards
Dina
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Please don't post (un)subscrib
Dear Prof.
Thank you very much from your help.
Best Regards
Dina
--
On 3/02/2012 3:17 AM, dina dusti wrote:
> Dear Prof
>
> Thank you very mu
Dear Gromacs Users,
I need to extract all possible distances between any two atom pairs of
a small hexa- to dodecamer from a trajectory.
The same is necessary for all dihedral angles of this protein. Now I
wonder if this is possible without defining all of them manually in
the ndx file and
Hello,
I have a system with 128 emi (cations) and 128 Cl (anions).
I want to calculate how many CL atoms are in cutoff distance relative to
hydorgen aotm of cation. I considered all CL atoms are distinguishable.
Basically I want to calcualte the distance between each CL atom and
correponing hyd
Dear Nilesh:
You don't seem to have made any progress since Mark gave you some
reading hints. Your best chance to get a useful response follows the
general form:
1. I want to do A.
2. I tried method B, here are the exact commands that I used (copy and paste)
3. With that method, I obtain C
Dear Mark
I want to calculate distance ca_ca from the third residue to the
ninth residue during MD .but i dont know identify in command number of
residue.
g_dist -f name.xtc -s topol.tpr -b 0 -e 20 -dt 0.002
and the second, can i get average distance by a command.
thanks for your advice
--
Hi all,
I want to calculate distance of protein residues by using g_dist, now I have
doubt that
1.Is it possible to calculate distance for more than two residues of two
comparable systems?
2. which type of group select for generating index file?_
Hi all user,
I have just calculated a distance between backbone and side chain of the same
protein. I get
negative distance along x and y direction. What dose negative distance mean?
Thanks in advance.
Abu Naser
School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [E
Hi there,
we are doing a pulling simulation and want to monitor the distance
between two atoms during pulling. Using g_dist the distance is
calculated between all mirror images of the periodic boundary
conditions, and the minimal distance is calculated. In our case, this
is uncomfortable,
Title: g_dist
Hi all
how reacts g_dist if one group contents 3 segments of three identical molecules. Are the distances calculated referring to the centers of mass of the single molecules segments and then averaged or referring to the center of mass of the set of the three segments?
Regards
Title: g_dist
Hi all
how does g_dist react if one group contents 3 segments of three identical molecules. Are the distances calculated referring to the centers of mass of the single molecules segments and then averaged or referring to the center of mass of the set of the three segments?
Rega
On 5/10/13 11:27 AM, mohammad agha wrote:
Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist, the
output is printed on the terminal, but I want them into a file as separately.
May I ask you to help me, Please?
Redirect the terminal output int
On 5/10/13 11:46 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your answer.
May I ask you to help me more, Please?
I work with UBUNTU, I don't know how should I do it!
Apply Google. This is not a Gromacs issue and should be investigated and
studied in the appropriate for
On 5/12/13 8:48 AM, mohammad agha wrote:
Dear GROMACS Specialists,
I want to obtain number of instances the different atoms was found within a
spherical shell of width 0.02 nm at a distance r
from the micelle COM. For this, I use g_dist -dist, but when I select for
example 0.04, it also resu
On 1/02/2012 1:05 AM, dina dusti wrote:
Dear Gromacs specialists,
Can you help me about g_dist?
I have a micelle system, I want to obtain distance between center of
mass of micelle with the last of carbon bounded to head group in
surfactant.
It should be near 2.2 but when I did "g_dist -f md
On 1/02/2012 4:26 PM, dina dusti wrote:
Dear Prof.
Thank you very much from your response.
Yes, dist.xvg has four column consists origin distance and distances
in direction x, y , z. So distance that I want according to result of
g_analyze, is 5.324286e-02 that isn't correct. I selected 2 grou
dina dusti wrote:
Dear Prof.
Thank you very much from your response.
Yes, dist.xvg has four column consists origin distance and distances in
direction x, y , z. So distance that I want according to result of
g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups,
micelle and the
dina dusti wrote:
Dear Prof.
Thank you very much from your response.
but I didn't select micelle headgroups and then terminal carbon atom but
also I selected COM of micelle and for example head group of micelle!
The calulation of radius of micelle by radius of gyration give that is
near 2.3
dina dusti wrote:
Dear Prof.
Thank you very much for your help.
Yes, I also used from g_rdf and g_gyrate but I am seeking
"root-mean-square distance" that there is in many articles for
calculation of radius of micelle and radius of dry core (hydrocarbone).
I understood that they used g_dist
dina dusti wrote:
Dear Prof.
Thank you very much from your response.
He answer me that I should use from g_gyration for radius of micelle,
but what should I do for hydrocarbon (dry) core or calculation of inner
core of micelle (i.e. the first of carbon on tail of surfactant with COM
of mice
st Regards
Dina
*From:* Justin A. Lemkul
*To:* dina dusti ; Discussion list for GROMACS
users
*Sent:* Thursday, February 2, 2012 12:08 AM
*Subject:* Re: [gmx-users] g_dist
dina dusti wrote:
> Dear Prof.
>
>
ion list for GROMACS
users
*Sent:* Thursday, February 2, 2012 2:42 PM
*Subject:* Re: [gmx-users] g_dist
dina dusti wrote:
> Dear Prof.
>
> Thank you very much from your response.
> OK, I use from g_gyrate for all of radius, but I still don't
understand that what thing did
dina dusti wrote:
Dear Prof
Thank you very much from your response.
She said me:
"In g_dist, when you select two groups for distance calculation, it
computes the distance between COM's of groups. Now, what is expected for
the distance between the micelle's COM and the COM of (e.g.) head
gro
On 3/02/2012 3:17 AM, dina dusti wrote:
Dear Prof
Thank you very much from your response.
She said me:
"In g_dist, when you select two groups for distance calculation, it
computes the distance between COM's of groups. Now, what is expected
for the distance between the micelle's COM and the COM
Steven Neumann wrote:
Dear gmx Users,
Can you please clarify me as I cannot find it anywhere what means the s0
legent in the dist.xvg as an outcome from g_dist? What is stated by |d|
? sx, sy, sz is the vector from two groups obviously.
It is the distance.
-Justin
--
=
Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the
data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfout,
both are 10 in this case) as given below
?Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the data
is printed at every 0.01 ps (according to pull_nstxout& pull_nstfout, both are
10 in this case) as given below
Hello,
I am seeking clarification on what this output means. I believe it
says that the x axis is divided into 4 time intervals and they are
plotted against a y axis that measures total distance along all 3
dimensional coordinates.
Am I reading this correctly?
# This file was created Sat Jan 30 0
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:
Dear Gromacs users,
I run my simulation for 20ns and want to extract aromatic-aromatic
distance to see the stacking issue. But I am unable to get the value.
I have 24 molecules in my simulation and filled with solvents.
My index file is like that:
[ System ]
123456
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the arch
Quoting shahrbanoo karbalaee <[EMAIL PROTECTED]>:
> Dear Mark
> I want to calculate distance ca_ca from the third residue to the
> ninth residue during MD .but i dont know identify in command number of
> residue.
Create an index group with those elements in it.
> g_dist -f name.xtc -s topol.t
minnale wrote:
Hi all,
I want to calculate distance of protein residues by using g_dist, now
I have doubt that
1.Is it possible to calculate distance for more than two residues of two
comparable systems?
g_dist calculates a simple center-of-mass distance between two points. What
kind o
Hi
I am doing MD-calculations on double layer lipid membranes. When I
wanted to calculate the distance between the com. of the lipids and my
molecule with g_dist, the program just stops! Sometimes directly and
sometimes after a couple of picoseconds. When checking the output it can
end like t
Hi again...
How can we tell? You haven't given us your command line, or a
meaningful chunk of output.
my command:
g_dist -f traj.xtc -n index.ndx -s topol.tpr
The output:
---
Select a group: 0
Selected 0: 'DPPC'
Select a group: 1
Selected 1: 'AL'
Reading frame 0 time0.000
Back
Naser, Md Abu wrote:
Hi all user,
I have just calculated a distance between backbone and side chain of the
same protein. I get
negative distance along x and y direction. What dose negative distance mean?
please be more specific. is that a vector?
Thanks in advance.
Abu Naser
School Of
]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Tue 25/09/2007 9:42 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist
Naser, Md Abu wrote:
>
>
> Hi all user,
>
&
: +44(0) 131 451 3009
-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Tue 25/09/2007 9:42 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist
Naser, Md Abu wrote:
>
>
> Hi all user,
>
> I have just calcul
)1314518265
Fax : +44(0) 131 451 3009
-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Tue 25/09/2007 9:42 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist
Naser, Md Abu wrote:
Hi all user,
I have just calculated a distance
Fax : +44(0) 131 451 3009
-Original Message-
From: [EMAIL PROTECTED] on behalf of Xavier Periole
Sent: Tue 25/09/2007 10:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist
On Tue, 25 Sep 2007 10:03:30 +0100
"Naser, Md Abu" <[EMAIL PROTECTED]
/09/2007 10:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist
On Tue, 25 Sep 2007 10:03:30 +0100
"Naser, Md Abu" <[EMAIL PROTECTED]> wrote:
Hi David,
Yes, it should be a vector as it is a difference between the center of mass
of two groups in
x,y,
] on behalf of Xavier Periole
Sent: Tue 25/09/2007 8:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist
The output of g_dist gives:
time distance DeltaX DeltaY DeltaZ
distance = sqrt(DeltaX**2+DeltaY**2+DeltaZ**2)
DeltaX, Y or Z are the differences of the atomic (COM
Kay Gottschalk wrote:
Hi there,
we are doing a pulling simulation and want to monitor the distance
between two atoms during pulling. Using g_dist the distance is
calculated between all mirror images of the periodic boundary
conditions, and the minimal distance is calculated. In our case,
They are not interacting. The distance is larger than 40 Å. But
still,if the distance to the mirror image is 41 Å and to the same
protein in the box is 45 Å, the distance to the mirror image will be
plotted... We are indeed pulling on z.
Best, Kay.
On May 22, 2006, at 6:02 PM, Xavier Periol
Kay Gottschalk wrote:
They are not interacting. The distance is larger than 40 Å. But
still,if the distance to the mirror image is 41 Å and to the same
protein in the box is 45 Å, the distance to the mirror image will be
plotted... We are indeed pulling on z.
Best, Kay.
Good, so the solu
yep, thanks!
K.
On May 22, 2006, at 6:15 PM, Xavier Periole wrote:
Kay Gottschalk wrote:
They are not interacting. The distance is larger than 40 Å. But
still,if the distance to the mirror image is 41 Å and to the same
protein in the box is 45 Å, the distance to the mirror image will
b
That'd certainly work if the movement is continuous,
but if there are many fluctuations near the crossover
point then sorting out which steps to fudge it at
could be a pain. Assuming you only care about the Z
seperation, I'd be tempted to use g_traj to plot both
groups, and subtract the z-position
I can also use VMD - not quite as comfortable as g_dist with the pbc
problem solved, but probably the quick and dirty 'fix', since I will
have to look at the trajectories anyway.
Thanks,
Kay.
On May 22, 2006, at 6:27 PM, Alan Dodd wrote:
That'd certainly work if the movement is continuous,
Alan Dodd wrote:
That'd certainly work if the movement is continuous,
but if there are many fluctuations near the crossover
point then sorting out which steps to fudge it at
could be a pain. Assuming you only care about the Z
seperation, I'd be tempted to use g_traj to plot both
groups, and sub
Dear Users,
I am trying to use g_dist to analize some dinamys. The problem is that
this program freeze just after selecting the to groups to calculate the
distance inbetween the mass centers with out any error and consuming
100% cpu. The versions with the problem are 3.3.x. The analasis using
Dear gromacs users,I have a comprehension question to g_dist with the lifetime(-lt) option.I want to determine the lifetime of a certain sidechain - ion contact (I use all ions as a group) within a radis of 0.6 nm.output:@ title "a_538 - K within 0.6 nm"@ xaxis label "Time (ps)"@ yaxis l
: Monday, April 23, 2012 3:59 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] g_dist explanation
Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the
data is printed at every
behalf
of Shilpi Chaurasia [shilpi.chaura...@unimi.it]
Sent: Monday, April 23, 2012 3:59 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] g_dist explanation
Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got
On 4/23/12 10:59 AM, Shilpi Chaurasia wrote:
Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the
data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfo
John Shultz wrote:
Hello,
I am seeking clarification on what this output means. I believe it
says that the x axis is divided into 4 time intervals and they are
plotted against a y axis that measures total distance along all 3
dimensional coordinates.
Am I reading this correctly?
There shoul
John Shultz wrote:
Here is what our script is doing. It looks to me like we are analyzing
the tpr when we should be checking the xtc or trr if I understand you
correctly. And if we look at the trajectory we can measure the drift
for the entire simulation rather than a specific instance.
The .
I tried using the xtc instead but it says the atom range is outside the index
g_dist -f md.xtc -s md.tpr -n index.ndx < protein_lig.txt
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VER
Here is what our script is doing. It looks to me like we are analyzing
the tpr when we should be checking the xtc or trr if I understand you
correctly. And if we look at the trajectory we can measure the drift
for the entire simulation rather than a specific instance.
make_ndx -f md.tpr < make_nd
Thank you Justin. The LIG was missing from our default mdp parameters.
That explains why we could not use the xtc file. I am adding it now.
On Tue, Mar 9, 2010 at 9:11 AM, Justin A. Lemkul wrote:
>
>
> John Shultz wrote:
>>
>> I tried using the xtc instead but it says the atom range is outside th
John Shultz wrote:
I tried using the xtc instead but it says the atom range is outside the index
Well, 3868 is the number of atoms in your protein, so I'm guessing you set
"xtc_grps = Protein" in the .mdp file. If you want to analyze other groups,
then you have to actually save their coor
How come time is always 0.000
On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul wrote:
>
>
> John Shultz wrote:
>>
>> Hello,
>>
>> I am seeking clarification on what this output means. I believe it
>> says that the x axis is divided into 4 time intervals and they are
>> plotted against a y ax
John Shultz wrote:
How come time is always 0.000
You're analyzing a .gro file, so there is no time information stored. If you
analyze a trajectory (i.e., .xtc or .trr), then the time is saved in the
individual frames.
-Justin
On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul wrot
Hi I am trying to post process and xtc trajectory using g_dist. I am trying
to calculate the CA-CB distance of an Alanine residue but I get NAN in all
the distance columns. It works for the other residues I've tried (i.e. SER,
VAL). I am using vsites in my simulation and I think it may have some th
Hi I am trying to post process and xtc trajectory using g_dist. I am trying
to calculate the CA-CB distance of an Alanine residue but I get NAN in all
the distance columns. It works for the other residues I've tried (i.e. SER,
VAL). I am using vsites in my simulation and I think it may have some th
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 gromacs Users,
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 .
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"
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
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
Edvin Erdtman wrote:
Hi
I am doing MD-calculations on double layer lipid membranes. When I
wanted to calculate the distance between the com. of the lipids and my
molecule with g_dist, the program just stops! Sometimes directly and
sometimes after a couple of picoseconds. When checking the out
Edvin Erdtman wrote:
Hi again...
How can we tell? You haven't given us your command line, or a
meaningful chunk of output.
my command:
g_dist -f traj.xtc -n index.ndx -s topol.tpr
The output:
---
Select a group: 0
Selected 0: 'DPPC'
Select a group: 1
Selected 1: 'AL'
Reading frame 0
David van der Spoel skrev:
Edvin Erdtman wrote:
Hi again...
How can we tell? You haven't given us your command line, or a
meaningful chunk of output.
my command:
g_dist -f traj.xtc -n index.ndx -s topol.tpr
The output:
---
Select a group: 0
Selected 0: 'DPPC'
Select a group: 1
Selected
Which compiler did you use?
This maybe says more:
$ file /usr/bin/g_dist
/usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1
(SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), stripped
-Edvin
___
gmx-users maili
Edvin Erdtman wrote:
Hi again...
How can we tell? You haven't given us your command line, or a
meaningful chunk of output.
my command:
g_dist -f traj.xtc -n index.ndx -s topol.tpr
The output:
---
Select a group: 0
Selected 0: 'DPPC'
Select a group: 1
Selected 1: 'AL'
Reading frame 0
Edvin Erdtman wrote:
Which compiler did you use?
This maybe says more:
$ file /usr/bin/g_dist
/usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1
(SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs),
stripped
I copied the file to another machine. And there g_di
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