[gmx-users] cant load trajectory, low memory

abhisek Mondal abhisek.mndl at gmail.com
Mon Apr 24 18:56:19 CEST 2017


Hello,

I'm using the configurations generated by pulling run to re-box > resolvate
> ion addition > EM > npt_umbrella(10ns) and forward.

So, please clarify me something. Am I following correct path ? Should I
have given a npt equilibration step prior to npt_umbrella step ?

Thank you.

On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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*
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> > > > --
> > > > Abhisek Mondal
> > > >
> > > > *Senior Research Fellow*
> > > >
> > > > *Structural Biology and Bioinformatics Division*
> > > > *CSIR-Indian Institute of Chemical Biology*
> > > >
> > > > *Kolkata 700032*
> > > >
> > > > *INDIA*
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> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*


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