[gmx-users] cant load trajectory, low memory

[Mark Abraham]

Hi,

Presumably that was discussed in the tutorial you were following. The Unix
diff tool can help with physically inspecting what is different between
those files. But really you should already know! A good rule of thumb is
not run a big calculation on expensive hardware
unless you know why you are doing it.

Mark

On Tue, 25 Apr 2017 12:13 abhisek Mondal <abhisek.mndl at gmail.com> wrote:

> Hi,
>
> I'm going with it.
>
> I still have a question. If I reconstruct the system (stripping the solvent
> and thus making smaller box size) I need to go through NVT>NPT
> equilibrations again. This part I got it.
> The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp
> will do ?
> What is the difference between running npt simulation with npt.mdp and
> npt_umbrella.mdp ?
>
> Please help me to catch up here.
>
> Thank you.
>
> On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/24/17 12:56 PM, abhisek Mondal wrote:
> >
> >> Hello,
> >>
> >> I'm using the configurations generated by pulling run to re-box >
> >> resolvate
> >>
> >>> ion addition > EM > npt_umbrella(10ns) and forward.
> >>>
> >>
> >> So, please clarify me something. Am I following correct path ? Should I
> >> have given a npt equilibration step prior to npt_umbrella step ?
> >>
> >>
> > Yes, as Mark said, you're essentially building all new simulation
> systems.
> > Since this is part of an umbrella sampling series, be sure you're getting
> > the same (or at least, very similar) number of water molecules in each
> box.
> >
> > -Justin
> >
> > Thank you.
> >>
> >> On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham <mark.j.abraham at gmail.com
> >
> >> wrote:
> >>
> >> Hi,
> >>>
> >>> I already answered that. You're effectively starting again, so do that.
> >>>
> >>> Mark
> >>>
> >>> On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal <
> abhisek.mndl at gmail.com>
> >>> wrote:
> >>>
> >>> Ok, I got it this time.
> >>>> But what kind of equilibration I'm to perform on these stripped
> >>>>
> >>> structures.
> >>>
> >>>> Should I perform normal NPT equilibration as done before generating
> >>>> configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c
> >>>>
> >>> conf0.gro
> >>>
> >>>> -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from
> tutorial
> >>>> page) and followed by mdrun step ?
> >>>>
> >>>>
> >>>> ....
> >>>
> >>>
> --
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