[gmx-users] entropy vs time plot

[tarak karmakar]

Dear Sir,

Thanks for the piece of script.
Bit modification and it works superbly.

thanks,
Tarak


On Wed, May 21, 2014 at 1:23 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2014-05-21 06:54, tarak karmakar wrote:
>
>> Hi Tsjerk,
>> Thanks for the quick reply.
>> I did the following
>>
>> g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v
>> eigenvec.trr -av average.pdb -b 0 -e 10000
>> g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 10000
>>
>> What I want to plot is similar to this.
>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/
>>
>> Is there any flag for this?
>> I've checked g_covar -h and g_anaeig -h but didn't get the proper way.
>>
>>  You need to run a
>
> for($N=1000; ($N<=10000); $N+= 100) {
> g_covar -e $N
> g_anaeig
> grep S from standard out and save it
>
> }
>
>
>  Thanks,
>> Tarak
>>
>>
>>
>> On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar <tsjerkw at gmail.com
>> >wrote:
>>
>>  Hi Tarak,
>>>
>>> You will have to use -b/-e to set the start and end times.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>> On Tue, May 20, 2014 at 12:18 PM, tarak karmakar <tarak20489 at gmail.com
>>>
>>>> wrote:
>>>>
>>>
>>>  Dear All,
>>>> Could anyone tell me how to plot configurational entropy as a function
>>>> of
>>>> simulation time?
>>>> Do I need to manually specify the -dt(say after each 1 ns) during the
>>>> g_covar and then do g_anaeig in each of the step?
>>>>
>>>> thanks,
>>>> Tarak
>>>> --
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>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
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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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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