2015-09-02 21:38 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 9/2/15 9:21 AM, Nawel Mele wrote: > >> 2015-09-02 14:09 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 9/2/15 8:48 AM, Nawel Mele wrote: >>> >>> 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?? >>>> >>>> >>>> Let's clear something up and make sure there is no misunderstanding. >>> When >>> I say "multiple runs" I am not simply referring to the fact that there >>> are >>> multiple simulations going on in REMD. That's obviously going on. What >>> I >>> mean is this: demux.pl processes a .log file and tells you when >>> exchanges >>> happen. So you need one .log file. If you have split your procedure >>> into >>> multiple *intervals of time* you will have multiple runs per replica, in >>> which case you need to concatenate the .log files *of one replica* to >>> pass >>> to demux.pl; if you did everything in one shot there is no need for >>> anything fancy and you just run demux.pl on one .log file. >>> >>> I hope this is clear. >>> >>> -Justin >>> >> >> >> Thank you very much. >> >> It is all clear. I have multiple "run" per replica because I can't >> performed my simulation in one shot. From that I will concatenate all the >> run for the replica I am interesting on and use this "concatenate log file >> " as input for demux.pl . >> The point I am not totally clear is , in order to produce a trajectory of >> all the "run" for one replica can I just do : >> >> trjcat -f *0_.trr -o R0_all.trr >> >> > Yes. > > In this point, if I don't need continuous trajectory I don't need to >> specify -demux replica_index.xvg option in the trjcat command? >> >> > Just be careful with the language. The trajectories *are* already > continuous with respect to ensemble. If you want them continuous with > respect to structures, then you need -demux. > > Thank you very much for your help, It is much more clearer now.
Nawel > > -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.
