Thanks for your email Justin. I remember you answered an email that there is a PRODRG server working with higher version of Gromos87. Could you show me the link please?
Also could you please give me the advice about other force field for my simulation? I am working with surfactants like alcohols, CTAB and triton x45. Best regards, Van On 5 December 2012 20:00, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/4/12 10:22 PM, cuong nguyen wrote: > >> Dear gmx users, >> >> i have got the coordinate and topol files of nonanol from the server: >> http://davapc1.bioch.dundee.**ac.uk/prodrg/submit.html<http://davapc1.bioch.dundee.ac.uk/prodrg/submit.html> >> >> the .gro file was download from option GROMOS87/GROMACS polar H's >> only<http://davapc1.bioch.**dundee.ac.uk/cgi-bin/xprodrg#**DRGPOH.GRO<http://davapc1.bioch.dundee.ac.uk/cgi-bin/xprodrg#DRGPOH.GRO> >> > >> >> and .top file was from >> optionGROMACS<http://davapc1.**bioch.dundee.ac.uk/cgi-bin/** >> xprodrg#DRGGMX.ITP<http://davapc1.bioch.dundee.ac.uk/cgi-bin/xprodrg#DRGGMX.ITP> >> > >> [D]<http://davapc1.bioch.**dundee.ac.uk/cgi-bin/xprodrg/** >> 50BEBB0C5FDC000078D6/asdl/**DRGGMX.ITP<http://davapc1.bioch.dundee.ac.uk/cgi-bin/xprodrg/50BEBB0C5FDC000078D6/asdl/DRGGMX.ITP> >> >(topology) >> >> >> Please let me know the name of this force field? >> >> > "GROMOS87/GROMACS" indicates the GROMOS87 force field in GROMACS format. > The GROMOS87 force field is deprecated, so you probably shouldn't be using > it since far better parameter sets exist. Also note that PRODRG topologies > are generally very inaccurate. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > 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> > -- 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