[gmx-users] cant load trajectory, low memory

[abhisek Mondal]

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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