Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint?
Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? Regards, Archana On Wed, Oct 23, 2013 at 5:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote: > >> Hi all, >> >> I have never performed TFE-water simulation therfore I want to know after >> inserting the peptide in the pre-equilibrated TFE-water mixture, do we >> need >> to adjust the number of TFE or water molecules ? >> >> > That depends on how you constructed the system. genbox will not > automatically update the number of TFE, but it can update the number of > water molecules if you chose the proper command-line option. Regardless, > the [molecules] section of the .top must accurately reflect the contents of > the configuration in terms of order and number of molecules. Simple grep > statements will let you count how many of each are present. > > -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 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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
