Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein
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 wrote: > Can you tell me of the constraint parameter u used and the corresponding > atom names > On 14 May 2016 00:11, "Tsjerk Wassenaar" 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 > > >> >> 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.
Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein
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 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 > > 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.
Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein
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 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.
Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein
Hi, Several things will make it easier to help - particularly your GROMACS versions and how you ran mdrun. See also http://www.gromacs.org/Support Mark On Fri, May 13, 2016 at 7:42 PM Antara mazumdar 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. > -- 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.
[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein
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.
