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Bug #169

trjconv's -ur option does not work

Added by Jellby empty about 12 years ago. Updated about 12 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

This bug refers to version 3.3.2, but it is not available in the list.

When trying use the -ur option of trjconv to view the simulation box with a different shape, it just doesn't work and always displays a rectangular box instead. With this example:

#!/bin/bash
echo "title">a.gro
echo "0">>a.gro
#the following is a single line:
echo " 3.44971 3.44971 2.43931 0.00000 0.00000 0.00000 0.00000 1.72486 1.72486" >> a.gro

genbox -cp a.gro -cs spc216.gro -o b.gro
pdb2gmx -f b.gro -p b.top -ff oplsaa
touch empty.mdp
grompp -f empty.mdp -p b.top -c b.gro -o b.tpr

echo 0 | trjconv -f b.gro -s b.tpr -ur compact -o c.gro

#End of script

the resulting c.gro is a rectangular box. It works fine (I get a dodecahedral box) if I use the trjconv program from a gromacs 3.3.1 install (the rest being the same).

History

#1 Updated by David van der Spoel about 12 years ago

There is an error in your script. The format of the box should be 9f10.5, you have the spaces incorrect. With the spaces corrected it works fine.

#2 Updated by Jellby empty about 12 years ago

OK, there was a mistake, but it still does not work for me and it worked with the trjconv from 3.3.1. To avoid more mistakes, I tried with this:

#!/bin/bash
touch a.pdb
editconf -bt dodecahedron -box 3.5 -f a.pdb -o a.gro
genbox -cp a.gro -cs spc216.gro -o b.gro
pdb2gmx -f b.gro -p b.top -ff oplsaa
touch empty.mdp
grompp -f empty.mdp -p b.top -c b.gro -o b.tpr
echo 0 | trjconv -f b.gro -s b.tpr -ur compact -o c.gro
#End of script

(with a.pdb and empty.mdp not existing before)

Again, it works with 3.3.1, it does not with 3.3.2.

I've just realized I'm not using the default gcc in my distribution, but a recent 4.3.0 build I had to install in order to use a newer gfortran (I thought only this gfortran was being used, but it appears also the newer gcc is). Still, both 3.3.1 and 3.3.2 are compiled with the same compiler.

#3 Updated by Jellby empty about 12 years ago

OK, I found the problem. I have to use "-pbc atom" (for example) in the trjconv command. This has changed with respect to 3.3.1.

However, I will fill a documentation bug, since the help text mentions an "inbox" option for -pbc, which is not recognized.

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