On 31/05/2012 7:46 PM, Acoot Brett wrote:
Hi Mark,
It is confusing. As you know, for the same hydrogen bond in a protein,
the related hydrogen bond angle and bond length can vary within a
scope during the whole simulation process, however this small
vibration of the hydrogen bond angle and length can lead to
significant energy change, and correspondingly the energy of a
hydrogen bond in simulation can be varied significantly. In comparison
with hydrophobic effect, it would be too much is the energy of the
hydrogen bond would be not calculated continuously.
It isn't, if the model physics isn't paramtrized to include it
explicitly - which is the case for all the force fields in GROMACS.
Could you give some further clarification?
What are trying to do? Measuring "the strength of a hydrogen bond"
requires you identify a state with and without it and a path between
them over which you can integrate.
Mark
Cheers,
Acoot
------------------------------------------------------------------------
*From:* Mark Abraham <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Thursday, 31 May 2012 4:48 PM
*Subject:* Re: [gmx-users] How GROMACS calculate the energy of
hydrogen bond
On 31/05/2012 4:42 PM, Acoot Brett wrote:
Dear All,
The value of the energy of the hydrogen bond has relation with
distance and angle of the hydrogen bond related atoms. As for in the
simulation process, the distance and angle of the hydrogen bond
related atoms may change continuously. Will you please let me know
based on which formula GROMACS calculated the value of the energy of
the hydrogen bonds?
There is no such formula used in MD force fields implemented in
GROMACS. The only non-bonded interactions are the ones you already
know about: electrostatics and VDW.
Observables like hydrogen bonds and the hydrophobic effect arise from
them.
Mark
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
