[gmx-users] cant load trajectory, low memory

[abhisek Mondal]

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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