2015-09-02 13:38 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 9/2/15 8:33 AM, Nawel Mele wrote: > >> Dear Justin, >> >> Thank you for your answer, >> >> So from the REMD simulation we get different output files: >> - .trr : trajectory file >> - .edr : energy file >> - .cpt: checkpoint used in case of crash >> - .log >> >> I am not use to perform REMD with gromacs so I am not sure which files do >> I >> need to concatenated to obtain my xvg trajectory. I assume is .trr because >> it is the trajectory file, but because it is a binary file I am not sure. >> >> > You should spend some time reading the manual and doing some tutorials. > > An .xvg is not a trajectory; it is a plain text data format. If you have > multiple intervals of time, you need to concatenate the .log files to > process via demux.pl - to provide you the information you (might) need, > you have to have information about the whole trajectory. >
> If I well understand you I don't need to use demux.pl to extract for >> example angle of my simulation at a certain temperature but using >> > > Correct. > > replica_temp.xvg file from the demux.pl file to evaluate if the lowest >> temperature go through all temperature space is incorrect ?? Should I >> > > Correct. > > create my own script with the *_0.log file to follow the temperature >> trajectory through temperature space? >> >> > I don't know why you think you need your own script; this is exactly what > demux.pl is for. > > In any case, properly invoking demux.pl depends on how you did the run. > If you ran everything in one interval, just: > > demux.pl md_0.log > > If you ran in multiple intervals: > > cat *_0.log > all.log (assuming you have md_0.log, md1_0.log, etc or some > such convention) > perl demux.pl all.log > I am use to perform simulation and specially REMD simulation with Amber software. But in Amber, exchanges in temperature space are accomplished by swapping temperature so a post processing is required to extract temperature trajectory. That's why I am a bit confused with Gromacs REMD. I know It must seems that I make you repeat but just to be sure, because I have multiple run I need to concatenate my .log files and then use this file into demux.pl to obtain information about the whole trajectory?? And from that I can do any kind of analysis I want?? Many thanks > > -Justin > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Nawel Mele, PhD Research Student Jonathan Essex Group, School of Chemistry University of Southampton, Highfield Southampton, SO17 1BJ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.