Dear GMX-users and developers,
I am interested in doing simulation of ibuprofen (NSAIDs Drug). But I am facing
some difficulties in getting the right topologies ( OPLS-AA force field). I get
my pdb field from PRODRG server.
Does anyone can help me in getting the correct file?
Any comments and
Hi all,
Is it right if running energy minimization using 4 nodes?
thanks for any comment
QIU YI HUAN
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Hi all,
Is it right if running energy minimization using 4 nodes?
thanks for any comments
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Hi all,
Is it right if running energy minimization using 4 nodes?
thanks for any comment
QIU YI HUAN
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Hi all,
Is it right if running energy minimization using 4 nodes?
thanks for any comment
QIU YI HUAN
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tein_G 1
Protein_H 1
T8092
QIU YI HUAN
A beginner of Gromacs user.
--- On Tue, 2/10/09, Justin A. Lemkul wrote:
> From: Justin A. Lemkul
> Subject: Re: [gmx-users] grompp error
> To: scottieh...@yahoo.com, "Discussion list for GROMACS use
Dear all.
I wanted to run grompp in order to perform Em, but it showed me this fatal
errer::
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter com
Dear Justin,
I didn't use any of the options.
I just use this command:
g_clustersize -f md1.xtc -s md1.tpr -n index.ndx -o -ow -nc -ac -mc .
all with default file name.
I didnt use other options.
Thanks a lot.
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LC2
> > WARNING 13 [file lipid.itp, line 108]:
> > Overriding non-bonded parameters,
> > old: 0.00238804 3.38411e-06 new
> > LNL C 1 2.387718e-03 2.389594e-06
> >
> -------
> > Program grompp, VERSION 4.0
>
ny
> Hsu)
>
>
> --
>
> Message: 1
> Date: Fri, 28 Nov 2008 12:24:52 +1100
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] defination of cluster
> To: Discussion list for GROMA
Dear all,
I did the g_clustsize to get the number of cluster graph for my system. At the
end of the simulation, the total number of cluster shown in the graph of my
system was 8. Then I had a view in the trjectory and I found that there were
total of 8 aggregated micelles and some free monome
Justin A. Lemkul <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] no density option in g_energy
> To: [EMAIL PROTECTED], "Discussion list for GROMACS users"
>
> Date: Thursday, November 27, 2008, 9:22 AM
> Q. Y. HUAN wrote:
> > Dear all, Why there is no de
Dear all,
Why there is no density option when I do g_energy amalyzation.
thanks
QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.
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Dear all,
After trjcat, I wish to view the combined trajactory using ngmx. The problem
is, how can i get the tpr combined file in oder to view the trajectory using
ngmx?
thanks for the help
QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.
_
Dear all ,
I did a simulation for 2 ns then i extanded the simulation using tpbconv for
another 2 ns. After that, I tried to combine the two trajectory files by using
trjcat by using the following command:
trjcat -f md1.xtc extend1.xtc -o combine.xtc
but it showed a warning that it couldn't rea
ect: Re: [gmx-users] average radius of gyration
> To: "Discussion list for GROMACS users"
> Date: Monday, November 24, 2008, 12:19 PM
> Q. Y. HUAN wrote:
> > Dear all,
> > I did g_gyrate and I obtained a gyration graph, then i
> did g_analyze with the following command:
Dear all,
I did g_gyrate and I obtained a gyration graph, then i did g_analyze with the
following command:
g_analyze -f gyration.xvg -av
Then I obtained a set of values as follow:
Read 4 sets of 201 points, dt = 10
std. dev.relative deviation of
Dear all gmx users and developers,
How can I generate a radial density graph ( density vs distance from center of
mass) ??
Can I analyze the moment of inertia of my system using Gromacs?
what tools should I use?
Any suggestions and comments will be greatly appreciated.
QIU YI HUAN
DEPARTMENT
Dear gmx users and developers,
Currently I am installing Grace into my computer, but the problem is that I
found difficulty to install it because there is no complete version of
installation file of it. After i installed the missing files, I install Grace
again but when I want to run xmgrace in
> From: Jochen Hub <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Repeating the simulation
> To: [EMAIL PROTECTED], "Discussion list for GROMACS users"
>
> Date: Thursday, November 6, 2008, 3:38 PM
> Q. Y. HUAN wrote:
> > Dear all gmx-users and developers,
&g
Dear all gmx-users and developers,
I have completed a simulation, and get all the results. Just asking you guys
for your opinion whether I should repeat the simulation again 1 or 2 times in
order to make sure the simulation results are valid for my work even thought I
have equilibrate my syste
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