[gmx-users] cant load trajectory, low memory

[Mark Abraham]

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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