[gmx-users] cant load trajectory, low memory

[Mark Abraham]

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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