[gmx-users] unfragmenting molecule in a trajectory

Irem Altan irem.altan at duke.edu
Wed Feb 1 22:56:54 CET 2017


Hi,

I was doing

gmx trjconv -f nvt.trr -s em.gro -pbc nojump -e 100 -dt 100 -o test.gro

I verify that em.gro is intact. nvt.trr is the output of a simulation whose .tpr file was created by a broken molecule. 

In any case, -pbc mol with the .tpr file works.

Best,
Irem

> On Feb 1, 2017, at 4:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 2/1/17 3:18 PM, Irem Altan wrote:
>> Hi,
>> 
>> For this I tried to do use the unfragmented configuration with the -s flag to trjconv when generating the trajectory. This results in a properly fragmented molecule, except for a single ILE residue. 3 atoms of this residue somehow remain displaced by the box size, while the other atoms of the same residue are correctly placed onto the protein. Is this a bug? If so, is there any way to circumvent it? (I use 5.1.2)
>> 
> 
> Without an exact sequence of commands, it's impossible to tell what may have happened.  It is extremely doubtful that trjconv has a bug in simple PBC routines.
> 
> Reconstructing "broken" molecules should be trivial with trjconv -pbc mol and a .tpr file passed to -s.
> 
> -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
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> https://urldefense.proofpoint.com/v2/url?u=http-3A__mackerell.umaryland.edu_-7Ejalemkul&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=11xfB38N1LYxHT_mAh2ohF-ThWQUO5iIbnlyemIJ_oA&s=6IwSx9Vp0pz6rDxSY06ktYRiIcvbBCLoP9WaHXZuIhI&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=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=11xfB38N1LYxHT_mAh2ohF-ThWQUO5iIbnlyemIJ_oA&s=BfsK71HmIphEaDylHmsmDUH2YP_HNHq29W6vnFqAzKk&e=  before posting!
> 
> * Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=11xfB38N1LYxHT_mAh2ohF-ThWQUO5iIbnlyemIJ_oA&s=PHH9uKNUxxZvrwMgeYj0Y90ziG7-S-9kieQu_Y4Kdqk&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=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=11xfB38N1LYxHT_mAh2ohF-ThWQUO5iIbnlyemIJ_oA&s=HiotTo0K1_6zUzFVgnbc8i37mXAg6DbHNfBNjoY0AT8&e=  or send a mail to gmx-users-request at gromacs.org.



More information about the gromacs.org_gmx-users mailing list