virtualchemistry.org has some topology files for many organic liquids.
Regards Rajesh On Tue, May 21, 2013 at 1:21 PM, Bao Kai <[email protected]> wrote: > Hi, > > Thank you for your response. > > I guess I took the problem wrong. I guess I need a topology file for > decane. > > I did some google search, generally people told that it can be done > manually, while this is really not my field. My field is CFD, while > my boss gave me some molecular simulation things to do. > > I am wondering if there is some more convenient way to generate the > the decane topology file. > > I found some .pdb file, while I failed to generate the .top file with > pdb2gmx. Generally the residue name is not correct. > > I wonder if there is anyone have done this before and would like to > provide one .top or .itp file on decane. Generally any forcefield > will work while OPLS-AA forcefield will be better. > > Thank you very much. > > Best Regards, > Kai > > > > > > On 4/16/13 6:51 AM, Bao Kai wrote: > >> Dear all, > >> > >> I am trying to do some two phase simulations with Decane molecules and > >> some > >> other smaller molecules. > >> > >> When I did simulations with smaller molecules, I specifies the > properties > >> based on each atom, while I just realized it is really not desirable to > >> do > >> it with Decane molecules ( 34 atoms each molecule). > >> > >> I am wondering if anyone could provide one coordinate file and the itp ( > >> or > >> .top ) file for the Decane simulation if you have ever done it before. > I > >> did not find very detailed Decane molecule models. > >> > > > > You should probably mention what force field you're trying to work with. > > For a > > simple alkane like decane, writing the necessary .rtp and .hdb (if > > necessary) > > entries is fairly trivial. Then just let pdb2gmx do all the work > assembling > > the > > whole topology. > > > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > > > > > ------------------------------ > > > > -- > > gmx-users mailing list > > [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > End of gmx-users Digest, Vol 108, Issue 106 > > ******************************************* > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Naga Rajesh Tummala, PhD Post-Doctoral Researcher, School of Chemistry and Biochemistry, Georgia Institute of Technology -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
