[gmx-users] cant load trajectory, low memory
abhisek Mondal
abhisek.mndl at gmail.com
Mon Apr 24 11:51:53 CEST 2017
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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