for example 530 ps instead of
1000 ps
-
Thanks again
Regards
D.M
From: Justin A. Lemkul
To: delara aghaie ; Discussion list for GROMACS users
Sent: Monday, 11 June 2012, 18:01
Subject: Re: [gmx-users] radius of gyration
On 6/11/12 9:28 AM
the terminal.
-Justin
Regards
D.M
*From:* Justin A. Lemkul
*To:* delara aghaie ; Discussion list for GROMACS users
*Sent:* Monday, 11 June 2012, 17:46
*Subject:* Re: [gmx-users] radius of gyration
On 6/11/12 9
?
Regards
D.M
From: Justin A. Lemkul
To: delara aghaie ; Discussion list for GROMACS users
Sent: Monday, 11 June 2012, 17:46
Subject: Re: [gmx-users] radius of gyration
On 6/11/12 9:09 AM, delara aghaie wrote:
> Dear Justin
> My question can be related t
On 6/11/12 9:09 AM, delara aghaie wrote:
Dear Justin
My question can be related to both. Ok let me talk about the tutorial. The
simulation has finished compeletly and log file and other outputs show the
completion of 1 ns simulation.
this is part of gyrate.xvg file I see:
-
@ s0 le
ed in?
Thanks for your time
Regards
D.M
From: Justin A. Lemkul
To: delara aghaie ; Discussion list for GROMACS users
Sent: Monday, 11 June 2012, 17:21
Subject: Re: [gmx-users] radius of gyration
On 6/11/12 8:40 AM, delara aghaie wrote:
>
On 6/11/12 8:40 AM, delara aghaie wrote:
Dear Justin.
Thanks for your explanation.
In lyzozyme tutorial the radius of gyration has been plooted against simulation
time (there 1000 ps).
When I plot the same graph, the horizontal axis i
Sent: Monday, 11 June 2012, 14:46
Subject: Re: [gmx-users] radius of gyration
On 6/11/12 5:20 AM, delara aghaie wrote:
> Dear Gromacs users
> I have a question abut radius of gyration in proteins. I want to calculate it
> via MD simulation for calcium pump protein. Following the same
On 6/11/12 5:20 AM, delara aghaie wrote:
Dear Gromacs users
I have a question abut radius of gyration in proteins. I want to calculate it
via MD simulation for calcium pump protein. Following the same method as
described in justin lezozyme tutorial, we have dissolved the protein in water.
I wan
Dear Gromacs users
I have a question abut radius of gyration in proteins. I want to
calculate it via MD simulation for calcium pump protein. Following the
same method as described in justin lezozyme tutorial, we have dissolved
the protein in water.
I want to know that is it wise to study this pa
Dear Gromacs users
I have a question abut radius of gyration in proteins. I want to calculate it
via MD simulation for calcium pump protein. Following the same method as
described in justin lezozyme tutorial, we have dissolved the protein in water.
I want to know that is it wise to study this par
Dear Justin,
Thank you very much from your response.
Best Regards
Dina
From: Justin A. Lemkul
To: dina dusti ; Discussion list for GROMACS users
Sent: Wednesday, May 9, 2012 4:52 AM
Subject: Re: [gmx-users] radius of gyration
On 5/8/12 4:50 PM, dina
On 5/8/12 4:50 PM, dina dusti wrote:
Dear Justin,
Thank you very much from your help, but may I ask you to say me why the error
estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand
any thing from paper about this problem!
The value of Rg is calculated from the (x,y
l
To: dina dusti ; Discussion list for GROMACS users
Sent: Wednesday, May 9, 2012 12:44 AM
Subject: Re: [gmx-users] radius of gyration
On 5/8/12 4:08 PM, dina dusti wrote:
> Dear Justin,
>
> Thank you very much from your help.
> Yes, the micelle was created after 100 ns from st
On 5/8/12 4:08 PM, dina dusti wrote:
Dear Justin,
Thank you very much from your help.
Yes, the micelle was created after 100 ns from start of simulation.
If the first procedure is true, so why the error estimate is so small and why
the error estimate of Rg is so different with Rg(x,y,z)?
Fo
Dear Justin,
Thank you very much from your help.
Yes, the micelle was created after 100 ns from start of simulation.
If the first procedure is true, so why the error estimate is so small and why
the error estimate of Rg is so different with Rg(x,y,z)?
Please help me.
Best Regards
Dina
--
gmx-us
On 5/8/12 1:06 PM, dina dusti wrote:
Dear GROMACS Specialists,
I have one question about radius of gyration for micelle, Please help me.
My micelle is created at 10 ps by Martini CG force field.
Does this mean that during the first 100 ns, there is no micelle? That is, it
is only compl
Dear GROMACS Specialists,
I have one question about radius of gyration for micelle, Please help me.
My micelle is created at 10 ps by Martini CG force field.
When I calculate the radius of gyration from this time as "g_gyrate -f 1.xtc -s
1.tpr -n 1.ndx -o gyrate.xvg -b 10" and "g_analyze
You understand correctly.
On Tue, Jun 21, 2011 at 11:35 AM, shahab shariati
wrote:
> Dear Tsjerk
>
> very thanks for your useful guidance.
>
> I now know that I should compare output of g_gyrate (containing Rg vs time)
> by area.xvg output file of g_sas (containing area vs time).
>
> In area.xvg
Dear Tsjerk
very thanks for your useful guidance.
I now know that I should compare output of g_gyrate (containing Rg vs time)
by area.xvg output file of g_sas (containing area vs time).
In area.xvg output file, there are several columns: "Hydrophobic",
"Hydrophilic" and "Total".
for example in
Hi Shahab,
When comparing two variables, they have to share an axis. Time for instance...
Cheers,
Tsjerk
On Tue, Jun 21, 2011 at 6:36 AM, shahab shariati
wrote:
> Dear Tsjerk
>
> thanks for your attention.
>
> larger radius of gyration, more surface. and smaller radius of
> gyration, less sur
Dear Tsjerk
thanks for your attention.
larger radius of gyration, more surface. and smaller radius of
gyration, less surface.
I want to obtain solvent accessible surface area using g_sas.
g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.
I will obtain three output files containing: area.xvg, resar
Dear Tsjerk
thanks for your attention.
larger radius of gyration, more surface. and smaller radius of
gyration, less surface.
I want to obtain solvent accessible surface area using g_sas.
g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.
I will obtain three output files containing: area.xvg, resar
Hey Shahab,
What's the contradiction?
> [ Furthermore, INT–DBD appears less compact in the complex, as far as the
> radius of gyration increases and more molecular surface is exposed to the
> solvent (Table 1). ]
larger radius of gyration, less compact, more surface
> [ Furthermore, according t
Dear all
I am studying md simulation of free protein and protein-ligand and
protein-dna complex.
In my simulation systems, the average of radius of gyration in free protein
is 2.31 and for protein in complex is 2.58.
I know the radius of gyration is measurement of compactness of the protein
as
s
Hi, C..
You wrote 1 ноября 2010 г., 22:09:36:
>
Does someone knows which equation is g_gyrate using to calculate the Rgx, Rgy,
Rgz components of the Rg and which is the relation between them?
I thougth that it was: Rg2=Rgx2+Rgy2+Rgz2, but at least for my results this is
not the case.
Sure,
Dear all
Does
someone knows which equation is g_gyrate using to calculate the Rgx,
Rgy, Rgz components of the Rg and which is the relation between them?
I thougth
that it was: Rg2=Rgx2+Rgy2+Rgz2,
but at least for my results
this is not the case.
Thanks a
lot
Chrysostomos
--
gmx-user
Johnny Lam wrote:
Hi all,
I am looking to equilibrate a peptide chain and I was wondering, is
there any way or any command that I can input into gromacs to make the
program output the radius of gyration data? Thanks a lot everyone!
g_gyrate.
-Justin
--Johnny
--
--
Johnny Lam wrote:
Hi all,
I am looking to equilibrate a peptide chain and I was wondering, is
there any way or any command that I can input into gromacs to make the
program output the radius of gyration data? Thanks a lot everyone!
you can analyze the trajectory using g_gyrate, but mdrun can
Hi all,
I am looking to equilibrate a peptide chain and I was wondering, is there
any way or any command that I can input into gromacs to make the program
output the radius of gyration data? Thanks a lot everyone!
--Johnny
--
-
Johnny Lam
ISPE Ber
Fabrizio Mancinelli wrote:
Dear users,
in computing radius of gyration of a protein in water (g_gyrate), I have
found values that are rather smaller than what found experimentally,
maybe because bound water isn't taken into account within g_gyrate
routine. Is there any way to overcome this lim
Dear users,
in computing radius of gyration of a protein in water (g_gyrate), I have
found values that are rather smaller than what found experimentally, maybe
because bound water isn't taken into account within g_gyrate routine. Is
there any way to overcome this limitation?
Thanks in advance,
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