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. -- 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
