Thanks for your earlier suggestions. I used the command g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.1 of (36.0, 36.0, 63.0)' -seltype res_com -selrpos res_com -os to find water molecule around a specified coordinate. But I get this error: Input error or input inconsistency: selection(s) could not be parsed
Would you please help me with this command? I have not yet tried g_select command. Thanks in advance. Sincerely, Shima ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sunday, July 7, 2013 9:45 PM Subject: Re: [gmx-users] Get some specific frames of traj On 7/7/13 1:14 PM, Shima Arasteh wrote: > Dear gmx users, > > I have a 10 ns simulation trajectory, and like to get some particular frames > of it. In fact I want to find the frames in which a specified coordinate is > filled with a water molecule, and then pick that frame as an initial > structure for the next steps. > > Is there any script implemented in GROMACS tools or any advantageous tool in > this approach? > g_select to find the frames of interest, then trjconv -dump to write them out. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
