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

[David van der Spoel]

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> 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> 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.
>> --
>> 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.
>


-- 
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    http://folding.bmc.uu.se