Re: [gmx-users] how to get the block averaged MSD curve ?
Well, I don't think excel will be a convenient tool for this. Why not
try awk for a change?
paste msd*.xvg | awk '/^[^@#;]/{S=0;N=0; for (i=2;i21; i+=2)
{S+=$i;N++}; print S/N}'
Otherwise a few lines of python would also do the trick.
Cheers,
Tsjerk
On Thu, Feb 9, 2012 at 1:56 PM, lina lina.lastn...@gmail.com wrote:
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim ilmare...@gmail.com wrote:
Hi,
I have a simulation result from 0 to 50ns after equilibration run.
I want to divide this data set equally into 10blocks (10ns each) and get
block averaged MSD curve (average of 10 blocks).
I would try some external software. excel.
It seems that I mange to get block MSD data by using g_msd -beginfit 0
-endfit 10, g_msd -beginfit 10 -endfit 20,
Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files)
My question is that how can I get averaged MSD from this outputs??
It seems that g_analyze is appropriate to do this.
g_analyze -n 10 -av ??
Could anybody tell me how to get averaged MSD using g_analyze (each block
data has different x values but same length) ?
Another question is that
what is the difference bwn g_msd and g_analyze -msd ??
Is there any reference of posting to obtain this information ?
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Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] how to get the block averaged MSD curve ?
On 2012-02-10 10:35, Tsjerk Wassenaar wrote:
Well, I don't think excel will be a convenient tool for this. Why not
try awk for a change?
paste msd*.xvg | awk '/^[^@#;]/{S=0;N=0; for (i=2;i21; i+=2)
{S+=$i;N++}; print S/N}'
Otherwise a few lines of python would also do the trick.
Cheers,
Tsjerk
On Thu, Feb 9, 2012 at 1:56 PM, linalina.lastn...@gmail.com wrote:
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kimilmare...@gmail.com wrote:
Hi,
I have a simulation result from 0 to 50ns after equilibration run.
I want to divide this data set equally into 10blocks (10ns each) and get
block averaged MSD curve (average of 10 blocks).
I would try some external software. excel.
g_msd -h
It seems that I mange to get block MSD data by using g_msd -beginfit 0
-endfit 10, g_msd -beginfit 10 -endfit 20,
Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files)
My question is that how can I get averaged MSD from this outputs??
It seems that g_analyze is appropriate to do this.
g_analyze -n 10 -av ??
Could anybody tell me how to get averaged MSD using g_analyze (each block
data has different x values but same length) ?
Another question is that
what is the difference bwn g_msd and g_analyze -msd ??
Is there any reference of posting to obtain this information ?
--
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] how to get the block averaged MSD curve ?
Hi, I have a simulation result from 0 to 50ns after equilibration run. I want to divide this data set equally into 10blocks (10ns each) and get block averaged MSD curve (average of 10 blocks). It seems that I mange to get block MSD data by using g_msd -beginfit 0 -endfit 10, g_msd -beginfit 10 -endfit 20, Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files) My question is that how can I get averaged MSD from this outputs?? It seems that g_analyze is appropriate to do this. g_analyze -n 10 -av ?? Could anybody tell me how to get averaged MSD using g_analyze (each block data has different x values but same length) ? Another question is that what is the difference bwn g_msd and g_analyze -msd ?? Is there any reference of posting to obtain this information ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to get the block averaged MSD curve ?
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim ilmare...@gmail.com wrote: Hi, I have a simulation result from 0 to 50ns after equilibration run. I want to divide this data set equally into 10blocks (10ns each) and get block averaged MSD curve (average of 10 blocks). I would try some external software. excel. It seems that I mange to get block MSD data by using g_msd -beginfit 0 -endfit 10, g_msd -beginfit 10 -endfit 20, Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files) My question is that how can I get averaged MSD from this outputs?? It seems that g_analyze is appropriate to do this. g_analyze -n 10 -av ?? Could anybody tell me how to get averaged MSD using g_analyze (each block data has different x values but same length) ? Another question is that what is the difference bwn g_msd and g_analyze -msd ?? Is there any reference of posting to obtain this information ? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
