how to go from (V1,V2,V3) to U1-U6 (GROMACS type)

Discussions on how to set up simulations, typically starting from a pdb file.
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ldav
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Joined: Wed Jul 23, 2008 9:38 am

how to go from (V1,V2,V3) to U1-U6 (GROMACS type)

Post by ldav » Thu Aug 07, 2008 2:26 pm

I use the following formulae to go from the V1-V3 (used in Hippo) to U1-U6 (used in GROMACS) with CA-CA-OH-HH as example:
------------------------------------------------------------
In Hippo: V1 V2 V3
For CA-CA-OH-HH : 0 1.682 0
In GROMACS U1 U2 U3 U4 U5 U6
For CA-CA-OH-HH : 7.037 0 -7.037 0 0 0
In Maestro: V1/2 V2/2 V3/2
For CA-CA-OH-HH : 0 0.841 0

From (V1,V2,V3) to (U1,U2,U3,U4,U5,U6):
U1 = (V2+(V1+V3)/2)*4.184
U2 = (3*V3-V1)*2.092
U3 = -V2*4.184
U4 = -2*V3*4.184
U5 = 0
U6 = 0
------------------------------------------------------------

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