[gmx-users] editconf
Dear GMX-Users, For understanding the aggregation propensity of the peptide I did a 1 us md simulation with periodic boundary. I defined a triclinic box around my peptide using editconf. The command I used is the following editconf -f tau_pep.gro -bt triclinic -d 1.1 -princ -o box.gro. Here -d 1.1 make any problems in the simulation?Is the value is appropriate? -- 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] REMD
Sir, I want to do an REMD simulation having 16 replicas. But I have only 8 processors. Is it possible to do 16 replicas in 8 processors? How I can do this? -- 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] cluster-PCA
Sir, I did 200 ns MD simulation. Now I want to project conformations from g_cluster onto principal component space.How can I do this? Thanks in advance.. -- 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] to study native cluster
Sir, I did an MD simulation.Now I want to combine the techniques, principal component (PC) analysis and clustering, for revealing major conformational changes in my protein and for finding native cluster. How can I do this in gromacs? Thanks in advance... -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_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
