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Big Water using insane.py
- Rajat Desikan
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9 years 4 weeks ago #4505
by Rajat Desikan
Big Water using insane.py was created by Rajat Desikan
Hi,
Is it possible to insert 10% of big water molecules into my system using insane (I am experiencing water freezing at 310 K in my membrane-protein-solvent system)?
This command failed:
python insane.py -l DLPC -a .55 -pbc rectangular -x 12 -y 12 -z 40 -f Martini_1-mer_1-176_box.gro -o Martini_1-mer_1-176_insane.gro -sol W:9 BW:1 -salt 0 -d 0
Is it possible to insert 10% of big water molecules into my system using insane (I am experiencing water freezing at 310 K in my membrane-protein-solvent system)?
This command failed:
python insane.py -l DLPC -a .55 -pbc rectangular -x 12 -y 12 -z 40 -f Martini_1-mer_1-176_box.gro -o Martini_1-mer_1-176_insane.gro -sol W:9 BW:1 -salt 0 -d 0
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- mnmelo
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9 years 4 weeks ago #4507
by mnmelo
Replied by mnmelo on topic Big Water using insane.py
Hi Rajat,
I'm not sure if insane.py is ready to admit multiple solvents, but you can always just have it output normal water and then force the BW into the topology.
Let's suppose you'd get 100 lipids and 1000 waters. You'd get a topology output like this:
DLPC 50
DLPC 50
W 1000
Simply change it to:
DLPC 50
DLPC 50
W 900
BW 100
grompp will complain that the atom names of those last 100 beads no longer match, but just use maxwarn to igrone it.
If you worry that by doing this the big waters will all be clumped together in the initial .gro file you can do one of the following:
-Allow the system to equilibrate for a couple of ns with 100% normal water. The waters will be mixed and you can then safely convert the last 10% to BW;
-Randomize the order of the waters in your initial .gro file. In vim's viusal mode you can select only the water lines of the .gro file and then issue ":'<,'>!sort -R" (without double quotes).
Good luck!
Manel
I'm not sure if insane.py is ready to admit multiple solvents, but you can always just have it output normal water and then force the BW into the topology.
Let's suppose you'd get 100 lipids and 1000 waters. You'd get a topology output like this:
DLPC 50
DLPC 50
W 1000
Simply change it to:
DLPC 50
DLPC 50
W 900
BW 100
grompp will complain that the atom names of those last 100 beads no longer match, but just use maxwarn to igrone it.
If you worry that by doing this the big waters will all be clumped together in the initial .gro file you can do one of the following:
-Allow the system to equilibrate for a couple of ns with 100% normal water. The waters will be mixed and you can then safely convert the last 10% to BW;
-Randomize the order of the waters in your initial .gro file. In vim's viusal mode you can select only the water lines of the .gro file and then issue ":'<,'>!sort -R" (without double quotes).
Good luck!
Manel
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- Rajat Desikan
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9 years 4 weeks ago #4509
by Rajat Desikan
Replied by Rajat Desikan on topic Big Water using insane.py
Thanks Manel,
Those suggestions worked wonderfully!
Regards,
Those suggestions worked wonderfully!
Regards,
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- tsjerk
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9 years 2 weeks ago #4515
by tsjerk
Replied by tsjerk on topic Big Water using insane.py
Hey,
A bit late, but for the record...
Insane does allow specifying multiple solvents, in the same way as it does for specifying lipids. However, antifreeze particles are not yet listed in insane (we'll fix that).
Insane randomizes the list of cells before filling them, so changing the type in the topology as suggested by Manel will result in a random distribution of BW particles.
Cheers,
Tsjerk
A bit late, but for the record...
Insane does allow specifying multiple solvents, in the same way as it does for specifying lipids. However, antifreeze particles are not yet listed in insane (we'll fix that).
Insane randomizes the list of cells before filling them, so changing the type in the topology as suggested by Manel will result in a random distribution of BW particles.
Cheers,
Tsjerk
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