When I do that it still reads from the beginning, saying “skipping frame”. I’ll divide the file in a few pieces and save all configurations. I’ll then cat the configs that I want. This is the simplest thing I can think of.
> On Jan 13, 2017, at 3:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 1/13/17 9:15 AM, Irem Altan wrote: >> I need to sample with logarithmic time intervals. >> > > Use -b to speed up moving through the trajectory before dumping the desired > time frame, or split the massive trajectory into smaller, more manageable > chunks that you can loop over simultaneously. > > -Justin > >> On Jan 13, 2017, at 3:12 PM, David van der Spoel >> <sp...@xray.bmc.uu.se<mailto:sp...@xray.bmc.uu.se>> wrote: >> >> On 13/01/17 14:41, Irem Altan wrote: >> Hi, >> >> So for some reason, the frame numbers I list won't match the timestamps when >> I use -fr. Is there a way to extract frames based on timestamps? The problem >> is, I want to be reading the file only once (or a few times), as it is huge >> (~500 GB), so I can’t use -dump by calling trjconv hundreds of times. >> >> How about the -dt flag? >> >> Best, >> Irem >> >> On Jan 13, 2017, at 2:31 PM, Mark Abraham >> <mark.j.abra...@gmail.com<mailto:mark.j.abra...@gmail.com>> wrote: >> >> Hi, >> >> Sadly there's nothing to be done except ignore the field or do multiple >> passes. The history of trjconv is a large number of people adding features >> convenient for their use case, and not knowing how it interacts with the >> huge surface area of the set of all other features. So the person who >> wanted such automatic regularisation trips the implementation of -fr, etc. >> >> Mark >> >> On Fri, 13 Jan 2017 14:22 Irem Altan >> <irem.al...@duke.edu<mailto:irem.al...@duke.edu>> wrote: >> >> Hi, >> >> I’m trying to extract a list of frames from a long trajectory: >> >> gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc >> atom -o conf_test.gro -sep >> >> where frames.ndx contains the following: >> >> [ frames ] >> 2 3 4 5 6 8 ... >> >> Each frame is supposed to be separated by 10 ps, so that for frame 2, t= >> 20.0000. Hence, conf_test1.gro starts with "Generated by trjconv : Protein >> in water t= 20.00000”, which is what we expect. However, the timestamps in >> the subsequent files are: >> >> Generated by trjconv : Protein in water t= 30.00000 >> Generated by trjconv : Protein in water t= 40.00000 >> Generated by trjconv : Protein in water t= 50.00000 >> Generated by trjconv : Protein in water t= 70.00000 >> Generated by trjconv : Protein in water t= 80.00000 >> … >> >> while it should have been 30, 40, 50, 60, 80, .... This happens a lot of >> times throughout the whole list of frames. Why does it happen? How can I >> fix it? >> >> Best, >> Irem >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ppIABLXb89vRNymMXHjuB7OKsEH9_ktC0F-3YJBGRuU&s=P_CtUW6Kfjof5MfEZPJPr6pRxEKUIhnzGSQxIk1Nhv0&e= >> before >> posting! >> >> * Can't post? 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