[gmx-users] RE: Is non-linear data output/storage possible?
nshafique at wesleyan.edu
Tue Jul 2 18:46:11 CEST 2013
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
I was thinking I would store data like this:
And then I would start another 'block' that would go
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
> Catch ya,
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> +61 3 9903 9304
> When the only tool you own is a hammer, every problem begins to resemble a
>> -----Original Message-----
> ] On Behalf Of Neha
>> Sent: Thursday, 6 June 2013 11:00 PM
>> 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
>> 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
>> 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
>> that energy/forces/coordinates are written and stored?
>> I understand the mdp files control the output, but I do not know how to
>> a non-linear output of data using nstxout etc. Please let me know if
>> have any ideas/have succeeded in getting Gromacs to do this!
>> View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-
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