[gmx-users] entropy vs time plot

[David van der Spoel]

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