[gmx-users] extracting a list of frames from a trajectory

[Irem Altan]

I need to sample with logarithmic time intervals.

On Jan 13, 2017, at 3:12 PM, David van der Spoel <spoel at xray.bmc.uu.se<mailto:spoel at 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.abraham at gmail.com<mailto:mark.j.abraham at 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.altan at duke.edu<mailto:irem.altan at 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? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ppIABLXb89vRNymMXHjuB7OKsEH9_ktC0F-3YJBGRuU&s=7Iimc_4yBcqJ3gLAG_mv4tzyzj5WnQqw9RXLcJPrwK8&e=

* For (un)subscribe requests visit
https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ppIABLXb89vRNymMXHjuB7OKsEH9_ktC0F-3YJBGRuU&s=8hcmv2pSfseIIQqIf4PNMI7VF9Jc6dF5n-FcCmYJvZA&e=  or
send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.
--
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? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ppIABLXb89vRNymMXHjuB7OKsEH9_ktC0F-3YJBGRuU&s=7Iimc_4yBcqJ3gLAG_mv4tzyzj5WnQqw9RXLcJPrwK8&e=

* For (un)subscribe requests visit
https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ppIABLXb89vRNymMXHjuB7OKsEH9_ktC0F-3YJBGRuU&s=8hcmv2pSfseIIQqIf4PNMI7VF9Jc6dF5n-FcCmYJvZA&e=  or send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se<mailto:spoel at xray.bmc.uu.se>    https://urldefense.proofpoint.com/v2/url?u=http-3A__folding.bmc.uu.se&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=AsxNLrIbuoW6ZToGPfLzlJvRCoTLFFvV3-vvpO0hdW0&s=lk3RPcIIQPNUpoCDeHxm9ZjGnMZZfUfkhwS3YBAU84k&e= --
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=AsxNLrIbuoW6ZToGPfLzlJvRCoTLFFvV3-vvpO0hdW0&s=YxZR3jgHEuZ89p4GTPassEgjeLT_UBLxHn8xT9srBcM&e=  before posting!

* Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=AsxNLrIbuoW6ZToGPfLzlJvRCoTLFFvV3-vvpO0hdW0&s=0fQOWMBz8J1baLZNmvT5GrOeoXCVzsxWscA9PPjqHc4&e=
* For (un)subscribe requests visit
https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=AsxNLrIbuoW6ZToGPfLzlJvRCoTLFFvV3-vvpO0hdW0&s=3VFQycmnmcuIGrXrIuhZaq0IIHdwBVhYvYrAEAYWee8&e=  or send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.