On 3/28/13 5:18 AM, 라지브간디 wrote:
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Dear Justin,
Thank for your pointing out my issues. I just want to know how it can be
converted.
I have referred the equation in chapter 4 and do not know exactly how I use
them.
For example, The C-O bond distance and force constant written as (0.112 and
3.7000e+07 ) in gromos, whereas in charmm27 written as ( 0.1128 and 933032.0).
I found the equation for g96 type covalent potential Vb (rij) and force
constant Fi(rij) and don't know how do i use this for above purpose?
Could you elaborate an example how it can be done? Thanks a lot.
Different force fields handle bonds in different ways. Gromos96 uses a quartic
bond potential (equation 4.36 in the manual), while CHARMM uses a normal
harmonic potential (equation 4.34). The data in ffbonded.itp are thus
interpreted differently, and in fact, when using a Gromos96 force field, the
square root of bond lengths are used, etc. If you multiply the CHARMM force
constant by 4, you arrive at the Gromos96 force constant (more or less). Note
that force constants are irrelevant if using constraints on these bonds.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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