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

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Mon Mar 19 10:28:07 CET 2012

Well... There is no mistake as for the option -t of grompp in the suggested version for this tutorial the file can be both trajcetory (trr) or a checkpoint file (cpt) from previous NVT ensemble. I hope you understand what you are doing?


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Acoot Brett [acootbrett at yahoo.com]
Sent: Monday, March 19, 2012 9:19 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] on -t nvt.cpt in the Justine Lemkul tutorial

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.



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