[gmx-users] Harmonic potential

[Andrey V Golovin]

Dear mn2,

May be that way :


editconf -scale 1 3 1
genbox -cs
editcond -o xxx.pdb

remove water that above some level by this awk script where some_y is
coordinate in box above that water should be removed

#!/bin/awk
( $3 != "HW1" && $3 != "HW2" ){print $5}
( $3 == "OW" && ($8 > some_y )){keep[$5]=0}
keep[$5]==1 {print $0} 

editconf -f xxx.pdb -o final.gro
-- 
Best regards, Andrey

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Andrey V. Golovin 
Ph.D,Professor assistant    tel: (095) 939-5305  
Bioengineering and 
Bioinformatics Department              
Moscow State University     fax: (095) 939-3181 
119899 Moscow            E-mail: golovin at genebee.msu.su 
Russia                      web: http://rnp-group.genebee.msu.su 
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