On Tue, Jul 2, 2013 at 12:46 PM, Neha <nshafi...@wesleyan.edu> wrote:
> 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. > > Actual copied and pasted commands, along with full .mdp files (or links to where they can be downloaded) would help a lot. With what we have on hand, all I could tell you is that something is wrong with your .mdp file(s). -Justin > > 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 > -- ========================================== Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- 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
