Dear Sir, I have used 1.8 rdd value.
Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- On Sat, May 14, 2016 at 12:14 AM, subhadip das <das.subhadi...@gmail.com> wrote: > Can you tell me of the constraint parameter u used and the corresponding > atom names > On 14 May 2016 00:11, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote: > >> Hi Antara, >> >> What commands did you use? At least make sure you add -rdd 1.6 to the >> command line of mdrun, because the default value is too small for coarse >> grain simulations. >> >> Cheers, >> >> Tsjerk >> >> On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar <antara.mazum...@igib.in >> > >> >> wrote: >> >> > Dear users, >> > >> > I am trying to run a coarse grained simulation of a membrane protein in >> a >> > mixed lipid billayer using martini model 2.2. I have already performed >> all >> > the equilibration steps successfully on my desktop with GROMACS 5.1.0. >> > However, when i try to execute its production run in parallel(having >> > gromacs 5.1 version installed) it complains of LINCS warning and >> > terminates at step 0. But on the contrary, it runs on the desktop >> > successfully. Kindly suggest something and please let me know if any >> more >> > information is required from my side. >> > >> > >> > Thanks!! >> > >> > Kind Regards, >> > Antara >> > >> > -- >> > Junior research fellow(project) >> > Systems biology group >> > CSIR-Institute of Genomics & Integrative Biology >> > South Campus >> > New Delhi - 110020 >> > M : +91-9717970040 >> > -- >> > >> > >> > >> > On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar < >> antara.mazum...@igib.in >> > > >> > wrote: >> > >> > > Dear gromacs users, >> > > >> > > I am trying to run a coarse grained simulation of a membrane protein >> in a >> > > mixed lipid billayer using martini model. I have already performed all >> > the >> > > equilibration steps successfully on my desktop. However, when i try to >> > > execute its production run in parallel it complains of LINCS warning >> and >> > > terminates at step 0. But on the contrary, it runs on the desktop >> > > successfully. Kindly suggest something and please let me know if any >> more >> > > information is required from my side. >> > > >> > > >> > > Thanks!! >> > > >> > > >> > > >> > > Kind Regards, >> > > Antara >> > > >> > > -- >> > > Junior research fellow(project) >> > > Systems biology group >> > > CSIR-Institute of Genomics & Integrative Biology >> > > South Campus >> > > New Delhi - 110020 >> > > M : +91-9717970040 >> > > -- >> > > >> > > >> > > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
