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genbox with update topology
- thu nguyen
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10 years 10 months ago - 10 years 10 months ago #1656
by thu nguyen
genbox with update topology was created by thu nguyen
Dear all,
Does MARTINI not update topology file automatically ? After i add water into system by using genbox, i have to update number of waters by hand. I used flag "-p topol.top" but it did not work.
Is there command help updating topology automatically ?
Best regards,
Thu
Does MARTINI not update topology file automatically ? After i add water into system by using genbox, i have to update number of waters by hand. I used flag "-p topol.top" but it did not work.
Is there command help updating topology automatically ?
Best regards,
Thu
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- jaakko
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10 years 10 months ago #1657
by jaakko
Replied by jaakko on topic genbox with update topology
Hi Thu,
genbox updates the topology file only in the case of atomistic water. ( http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation ) For all other atomistic solvents and for all coarse-grained solvents you need to modify the file manually.
Cheers,
Jaakko
genbox updates the topology file only in the case of atomistic water. ( http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation ) For all other atomistic solvents and for all coarse-grained solvents you need to modify the file manually.
Cheers,
Jaakko
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- thu nguyen
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10 years 10 months ago #1659
by thu nguyen
Replied by thu nguyen on topic genbox with update topology
Thank Jaakko so much !
But it's very inconvenient when simulating many systems in the same time. Is there any script for updating solvents automatically ? I searched in google, but may i used bad key words. I did not find the right script
But it's very inconvenient when simulating many systems in the same time. Is there any script for updating solvents automatically ? I searched in google, but may i used bad key words. I did not find the right script
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- xavier
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10 years 10 months ago #1681
by xavier
Replied by xavier on topic genbox with update topology
No, no script to do it automatically but it would not be too hard to write a shell script to do this ...
thu nguyen wrote: Thank Jaakko so much !
But it's very inconvenient when simulating many systems in the same time. Is there any script for updating solvents automatically ? I searched in google, but may i used bad key words. I did not find the right script
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