[gmx-users] on -t nvt.cpt in the Justine Lemkul tutorial

[Tsjerk Wassenaar]

Hi Acoot,

It's correct. Checkpoint files (.cpt) were not available in versions
<4. Just like the v-rescale thermostat was not available. For many
purposes the checkpoint file can be regarded similar to a trajectory
though, so replacing nvt.cpt by nvt.trr works properly for version
3.3.3.

Cheers,

Tsjerk

On Mon, Mar 19, 2012 at 10:19 AM, Acoot Brett <acootbrett at yahoo.com> wrote:
> Dear All,
>
> I am using the GROMACS 3.3.3 to practice the lysozyme tutorial of Justin
> Lemkul
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html.
>
> For the final part grompps, for example "grompp -f npt.mdp -c nvt.gro -t
> nvt.cpt -p topol.top -o npt.tpr", it shows the nvt.cpt.trr. cannot be read.
> Then I change "grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o
> npt.tpr" into "grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -o
> npt.tpr", it works.
>
> I am looking a clarification from you that my change is correct.
>
> Cheers,
>
>
> Acoot
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands