Yes, Thanks. Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings? To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US?
Many many thanks for your time and suggestions. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, July 24, 2013 8:05 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:30 AM, Shima Arasteh wrote: > Hi, > > I am trying to run US on a system composed of lipid bilayer/ ion/ water/ > peptide. The peptide is inserted through the lipid bilayer and I' d like to > study the ion conduction through the peptide across the membrane. > > In order to do so, I tried to set a specific ion ( Ces with the atom number > 85563) as the pull_group1 in mdp file: > pull_group1 = Ces_ion > > So I had to get a new group named Ces_ion contains of Ces 85563. Therefore > made a new index file ( index_US.ndx). In this ndx file, there is an extra > group in addition of existed groups as this( The last 2 lines in ndx file) : > > [ system] > ... > [protein] > ... > [protein-H] > ... > > > [ Ces_ion ] > 85563 > > But after running the grompp, I get this fatal error: > File input/output error: > index_US.ndx > > > Would you please let me know how I would be able to define a new group for a > specific ion ? > Did I make a mistake in defining a new group? What you did in terms of index group content is fine. The error message means that the file called "index_US.ndx" is not present in the working directory, or it has the wrong permissions. -Justin -- ================================================== Justin A. Lemkul, Ph.D. 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 ================================================== -- 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
