Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sun, 26 Dec 2010 10:59:22 -0800

> 1) the length of O-H bonds are longer than those of normal waters. 2) there
> are new bonds between H atoms
> of each water
> molecule.

What is the length of the OW-HW bond, and what do you expect? It
should be exactly what the FF specifies, assuming you used SHAKE

In TIP3P, a bond is made between the water H's to keep the water
rigid, so if you were using TIP3P in GROMACS, there should have
been the H-H bond there, too.


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Received on Sun Dec 26 2010 - 11:30:04 PST
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