[gmx-users] RE: Is non-linear data output/storage possible?

[Neha]

So I tried doing this and ran into another problem.

I made two mdp files, one that stored data every ten steps and one every
hundred steps 

I was thinking I would store data like this:

10
20 
30
.
.
.
100
200
.
.
.
1000

And then I would start another 'block' that would go 

1010
1020
.
.
.
1100
1200
.
.
.
2000

I am able to get one block of data stored the way I want. However when I use
grompp to extend the simulation from that block using the mdp file that
would store data every 10 time steps once again, I get a warning that the
run will generate an obscene amount of data and that the simulation is
running for infinite ps. I am not sure why that is happening and was
wondering if anyone had any ideas as to how to fix it. Or better yet, if
someone else has a way to do this kind of non-linear data storage that has
not occurred to me yet.

Let me know if you need anymore information, I understand that this might be
confusing to follow.


Dallas Warren wrote
> Easiest, naïve way that I can see is to do the simulation in blocks, and
> change the output settings within the mdp file used as required for each
> block.
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052

> dallas.warren@

> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail. 
> 
> 
>> -----Original Message-----
>> From: 

> gmx-users-bounces@

>  [mailto:gmx-users-
>> 

> bounces@

> ] On Behalf Of Neha
>> Sent: Thursday, 6 June 2013 11:00 PM
>> To: 

> gmx-users@

>> Subject: [gmx-users] Is non-linear data output/storage possible?
>> 
>> Hi everybody!
>> 
>> This is a sort-of general question that I am not sure where to find the
>> answer for. I am running a simulation on the order of tens of
>> microseconds.
>> However I also want to do some analysis on the order of very small time
>> steps but I do not want to save the data of very small time steps
>> throughout
>> the length of the simulation as it will be taxing for the memory. I was
>> wondering if there was a way to be able to store small time steps for a
>> small time during the simulation and continue to increase the amount of
>> time
>> that energy/forces/coordinates are written and stored?
>> 
>> I understand the mdp files control the output, but I do not know how to
>> have
>> a non-linear output of data using nstxout etc. Please let me know if
>> you
>> have any ideas/have succeeded in getting Gromacs to do this!
>> 
>> 
>> 
>> --
>> View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-
>> linear-data-output-storage-possible-tp5008858.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>> --
>> gmx-users mailing list    

> gmx-users@

>> 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-request@

> .
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    

> gmx-users@

> 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-request@

> .
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists





--
View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-linear-data-output-storage-possible-tp5008858p5009506.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.