Dear justin Thank you for your rely and precious time.
I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.gro )file by running the command of energy minimization i.e. "mdrun -v -deffnm em" and before this command I ran the command "perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat" after running the energy minimization the confout.gro is actually obetained as confout.gro.trr. so I am renaming it as confout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Please help. On Tue, Sep 30, 2014 at 4:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/30/14 7:06 AM, Anurag Dobhal wrote: > >> Thank you Justin for your reply >> >> as per your suggestion i verified the contents in confout.gro but i was >> unable to check file as when i am clicking on it to open it I am getting >> an >> message that file is of unknown type. >> >> > A .gro file is not simply something that you click on to magically open. > It's just a listing of coordinates. Visualize it in VMD. Inspect its > contents with a text editor. > > -Justin > > > I again repeated the tutorial and I am getting the same things. >> >> Thank you again for your time. >> >> On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 9/30/14 5:51 AM, Anurag Dobhal wrote: >>> >>> Hello gromacs users. >>>> >>>> >>>> I am running GROMACS Tutorial of KALP15 in DPPC. >>>> >>>> I am in the step define box and solvate. >>>> >>>> after the command >>>> >>>> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 >>>> area_shrink1.dat >>>> >>>> >>>> i am getting an error as >>>> >>>> Use of uninitialized value $box_x in multiplication (*) at >>>> inflategro.pl line 339. >>>> Use of uninitialized value $box_y in multiplication (*) at >>>> inflategro.pl line 340. >>>> Scaling lipids.... >>>> There are 0 lipids... >>>> Illegal division by zero at inflategro.pl line 380. >>>> >>>> I am repeating the step third time and I am getting the same error. >>>> >>>> please help me how to skip this error. >>>> >>>> >>>> I suggested you verify the contents of confout.gro are sensible. What >>> did >>> you learn? >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> 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? 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