If you are taking confout.gro as your starting input file, it will have all water and ions of the previous simulation.
On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar <tasneemkausa...@gmail.com> wrote: > Create index group that have both protein and ACO. gmx make_ndx will serve > this task. > Then create a pdb file file from gmx trjconv > Or you can choose system as output and delete ions and solvent from any > editor. > > > > On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal <abhisek.m...@gmail.com> > wrote: > >> Hello, >> >> Alright. I have tried this but I'm stuck in the following scenario. >> I'm using trjconv for getting pdb file of the protein-ligand complex (used >> for umbrella sampling). >> trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr >> >> This is giving me the following prompt: >> Select group for output >> Group 0 ( System) has 27051263 elements >> Group 1 ( Protein) has 1588 elements >> Group 2 ( Protein-H) has 1245 elements >> Group 3 ( C-alpha) has 158 elements >> Group 4 ( Backbone) has 474 elements >> Group 5 ( MainChain) has 633 elements >> Group 6 ( MainChain+Cb) has 784 elements >> Group 7 ( MainChain+H) has 785 elements >> Group 8 ( SideChain) has 803 elements >> Group 9 ( SideChain-H) has 612 elements >> Group 10 ( Prot-Masses) has 1588 elements >> Group 11 ( non-Protein) has 27049675 elements >> Group 12 ( Other) has 59 elements >> Group 13 ( ACO) has 59 elements >> Group 14 ( NA) has 16615 elements >> Group 15 ( CL) has 16615 elements >> Group 16 ( Water) has 27016386 elements >> Group 17 ( SOL) has 27016386 elements >> Group 18 ( non-Water) has 34877 elements >> Group 19 ( Ion) has 33230 elements >> Group 20 ( ACO) has 59 elements >> Group 21 ( NA) has 16615 elements >> Group 22 ( CL) has 16615 elements >> Group 23 ( Water_and_ions) has 27049616 elements >> Group 24 ( >> >> Now how can I be able to get both Protein+ACO as a pdb file ? >> If I could get Protein+ACO, then I could strip the box size for further >> umbrella sampling procedure. >> >> However, is it possible to go with the following way: >> editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic >> >> Please suggest me a way. >> >> Thank you. >> >> On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham <mark.j.abra...@gmail.com> >> wrote: >> >> > Hi, >> > >> > Take a configuration of interest, strip the solvent, put it in a box you >> > think is good, and re-equilibrate just like you did before you started. >> > >> > Mark >> > >> > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <abhisek.m...@gmail.com> >> > wrote: >> > >> > > Hi, >> > > >> > > Yes, I did when I started the simulation. The box size I used to start >> > the >> > > simulation was very big(I was dealing with an unknown sample). After >> > > successfully generating the configurations I realized that further >> work >> > > could move faster if I could trim the box size little bit now. >> > > So is there any way now to reduce the box size and proceed with >> relevant >> > > configurations towards PMF generation ? >> > > Please suggest me a way here. >> > > >> > > Thank you. >> > > >> > > On Apr 24, 2017 12:22 AM, "Mark Abraham" <mark.j.abra...@gmail.com> >> > wrote: >> > > >> > > > Hi, >> > > > >> > > > You get to choose the box size eg with editconf when you set up your >> > > > simulation. It's not pre-defined ;-) >> > > > >> > > > Mark >> > > > >> > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal <abhisek.m...@gmail.com> >> > wrote: >> > > > >> > > > > Hello, >> > > > > >> > > > > Another thing I wanted to ask. >> > > > > After generating configurations I found out that the predefined >> box >> > > size >> > > > > (used to reach so far) is excessively high. >> > > > > Is it possible to trim the box size to perform further mdrun >> during >> > > > > umbrella sampling? >> > > > > >> > > > > Please suggest me a way, it is taking very long time with current >> box >> > > > size. >> > > > > >> > > > > Thank you. >> > > > > >> > > > > >> > > > > >> > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham" < >> mark.j.abra...@gmail.com> >> > > > wrote: >> > > > > >> > > > > > Hi, >> > > > > > >> > > > > > You can only load a trajectory with fewer frames. Either don't >> > write >> > > so >> > > > > > many, or filter it with trjconv first. >> > > > > > >> > > > > > Mark >> > > > > > >> > > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal < >> abhisek.m...@gmail.com> >> > > > wrote: >> > > > > > >> > > > > > > Hi, >> > > > > > > I'm having a problem loading trajectory file after umbrella >> > > sampling. >> > > > > The >> > > > > > > file is so huge in size that the VMD finally runs out of >> memory. >> > > I'm >> > > > > > > operating with 125gb of physical memory here though. >> > > > > > > >> > > > > > > Is there any way out of it ? >> > > > > > > >> > > > > > > >> > > > > > > Thank you >> > > > > > > -- >> > > > > > > Abhisek Mondal >> > > > > > > >> > > > > > > *Senior Research Fellow* >> > > > > > > >> > > > > > > *Structural Biology and Bioinformatics Division* >> > > > > > > *CSIR-Indian Institute of Chemical Biology* >> > > > > > > >> > > > > > > *Kolkata 700032* >> > > > > > > >> > > > > > > *INDIA* >> > > > > > > -- >> > > > > > > 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? 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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. >> > > >> > -- >> > 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. >> > >> >> >> >> -- >> Abhisek Mondal >> >> *Senior Research Fellow* >> >> *Structural Biology and Bioinformatics Division* >> *CSIR-Indian Institute of Chemical Biology* >> >> *Kolkata 700032* >> >> *INDIA* >> -- >> 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? 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