Hi Justin, Thanks...it was really helpful. I saw the http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site.
Now I don't know how to calculate the number of cosolvents (in my case TFE for TFE-water in 1:1 vol). Is there any formula to carry out this calculation. I can follow other mentioned steps. Thanks in advance. On Wed, Jul 17, 2013 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote: >> >> HI, >> >> I want to simulate helical peptide in TFE-water (1:1 vol) solvent. >> >> 1. From previous searches, I got to know that tfe.itp is present in >> gmx.ff folder. Can I use this itp file by including it in my top file >> generated during pdb2gmx. >> > > Since that file requires the use of the deprecated (i.e. don't use it) > gmx.ff force field, I wouldn't. > > >> 2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrated system >> from ATB site. I dont know if I can use either this pdb or gro file >> during genbox step for -cs flag >> > > Sure, if it suits your purpose. See also > http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents. > > -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 -- 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
