try ptraj
Date: Fri, 15 Jun 2012 10:18:40 +0400
Subject: Re: [gmx-users] analysing of the long trajectories
From: jmsstarli...@gmail.com
To: gmx-users@gromacs.org
By the way,
I'm also looking for a most trivial way for extraction of pdb files from my
trajectory on the desired intervals. E.g I
29 May 2012 18:48:15 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] How to install GROMACS in 64-bit?
On 29/05/2012 6:37 PM, a a wrote:
Dear Sir/Madam,
Thanks for the insightful comme
Dear Sir/Madam,
Thanks for the insightful comments from the experts.Follows the steps, I
found the source of error:
This what I have done:
In the following directory
/home/softwares/fftw-3.0.1:./configure --enable-shared
--prefix=/home/sof
Dear Sir/Madam,
Follow the steps below, I have installed fftw library and gromacs as a root.
(1) tar -xzvf fftw-3.0.1.tar.gz(2) cd fftw-3.0.1(3) ./configure --enable-float
--enable-threads --enable-shared(4) make(5) make install(6) tar -xzvf
gromacs-4.5.5.tar.gz(7) cd gromacs-4.5.5(8) ./confi
Thank you Roland,
It works now.
Best regards,
Catherine
From: rol...@utk.edu
Date: Sat, 26 May 2012 16:04:53 -0400
Subject: Re: [gmx-users] How to read in netcdf with GROMACS?
To: gmx-users@gromacs.org
Hi,
On Sat, May 26, 2012 at 12:42 PM, a a wrote:
/usr/local/lib/vmd/plugins
Dear Sir/Madam,
I am trying to do the following analysis with GROMACS:
/usr/local/gromacs/bin/g_covar -s my.pdb -f my.netcdf -o -v
However, I found the following error message:
-
Thank you very much Tsjerk,
I under cosine content much better now.
When you means "that only makes sense for one Pc, the analysis is thus
performed per component", could you mind to explain more?
I did the cosine content analysis with the following command "
/usr/local/gromacs/bin/g_analyze_d
Dear experts in the field,
When we use cosine content to determine if our simulation are converged or not,
should I
(1) sum all the first three principal components together or examine
individually?
(2) If I expect the first 10 ns is the equilbrium period, while the other 20 ns
as the producti
content. But that can't be
> turned around! I can think of a lot of lines that don't match well
> with a cosine, but that are inconsistent with convergence.
>
> That said, the index in the .xvg file is the principal component
> index. So the projection on the first pc has a c
Dear Sir/Madam,
I used the following steps to get the cosine content for my trajectories, could
you please kindly tell me how to interpret the results?
/usr/local/gromacs/bin/g_covar_d -s ../test.pdb -f test.binpos -o -v
/usr/local/gromacs/bin/g_anaeig_d -s ../test.pdb -f test.binpos -v eigenvec.
Dear Sir/Madam,
I have problem to read in mdcrd files.
I followed the procedures in the manual to
(1) installed VERSION 4.5.5 gromacs
(2) installed VMD
(3) in the .bashrc file, I added a line
export VMD_PLUGIN_PATH=/home/vmd_ied/lib/vmd/plugins/LINUX/molfile
(4) In the above molfile, I got all t
Dear Sir/Madam,
I am trying to run covar using mdcrd file.
I installed the vmd and gromacs 4.5.5. to my computer. I also set the
VMD_PLUGIN_PATH by adding a line in .bashrc file in my home directory.
VMD_PLUGIN_PATH=/home/cmche/AnnieSoftwares/vmd_ied/lib/vmd/plugins/LINUX/molfile
When I did the f
Dear experts,
I am trying to do the following command:
/usr/local/gromacs/bin/g_covar_d -s test.pdb -f test.mdcrd -o -v
But the following error message is found:
---Program g_covar_d,
VERSION 4.5.5Source code file: trxio.c, line: 870
Fatal error
Dear Sir,
I am using g_covar version 4.0.7.
I am trying to do:
/share1/gromacs/bin/g_covar -s ../average.pdb -f ../md0.binpos -o -v
However, an error message appear:
Program g_covar, VERSION 4.0.7Source code file: gmxfio.c, line: 737
Can not open file:../md0.mdcrd.xtc
What should I do next?
Best
MACS.
On 9/03/2012 10:58 PM, a a wrote:
Dear Sir/Madam,
I am trying to install the GROMACS to my new
workstation. As my old one is not belong to me, I cannot
install VMD t
Dear Sir/Madam,
I am trying to install the GROMACS to my new workstation. As my old one is not
belong to me, I cannot install VMD to it. Please kindly help to instruct if I
did anything wrong here. Many thanks.
Follow the steps in http://www.cems.uvm.edu/~smanchu/gromacs_installation.html,
I
Dear Sir/Madam,
I learnt that we can use mdcrd from AMBER directly.
I have used the following commands.
/share1/gromacs/bin/g_covar -s xxx.pdb -f xxx.mdcrd -o -v
An error message was obtained.
Program g_covar, VERSION 4.0.7Source code file: gmxfio.c, line: 737
Can not open file:md0.mdcrd.xtc
Did I
,
Catherine
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Date: Thu, 8 Mar 2012 21:36:03 +1100
Subject: Re: [gmx-users] How to input multiple trr files?
On 08/03/12, a a wrote:
Dear Gromacs experts,
I am trying to use the following command:
g_covar -s file.pdb -f dynamic.trr -o -v
Dear Gromacs experts,
I did the following steps to calculate the cosine content for my MD simulation.
> g_covar -s file.pdb -f dynamic.trr -o -v> g_anaeig -s file.pdb -f dynamic.trr
> -v eigvect.trr -proj> g_analyze -f proj.xvy -cc -n 8
After the final step, I got a file call "coscont.xvg",
Dear Gromacs experts,
I am trying to use the following command:
g_covar -s file.pdb -f dynamic.trr -o -v
However, since my trr file is too large, I have to separately prepared it into
dynamic1.trr dynamic2.trr, dynamic3.trr.
Would you mind to instruct how to input several trr files, how to mo
Dear Gromacs experts,
How to calculate the cosine content of a trajectory?
Best regards,
Catherine --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/S
Dear Gromacs experts,
How to read AMBER's mdcrd files with GROMACS? Many thanks again for your help.
Best regards,
Catherine
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