[gmx-users] cant load trajectory, low memory
Mark Abraham
mark.j.abraham at gmail.com
Mon Apr 24 12:56:25 CEST 2017
Hi,
I already answered that. You're effectively starting again, so do that.
Mark
On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal <abhisek.mndl at gmail.com>
wrote:
> Ok, I got it this time.
> But what kind of equilibration I'm to perform on these stripped structures.
> Should I perform normal NPT equilibration as done before generating
> configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c conf0.gro
> -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from tutorial
> page) and followed by mdrun step ?
>
>
>
>
> On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar <tasneemkausar12 at 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.mndl at 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.abraham at 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.mndl at 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.abraham at 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.mndl at 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.abraham at 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.mndl at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list