See section 5.7.1 of the manual , it shows you exactly how you define angles, bond, dihedrals etc for any type of molecule in the topology files for GROMACS. If after the theory, see section 4.2
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of udaya dahal Sent: Tuesday, 20 April 2010 10:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] help Respected Sir/Madam, I am student of Tribhuwan University and trying to find out diffusion coefficient of D2O in H2O. But due to lack of access of journal i am not being able to complete my job. Can any tell me how to define angle in the topology file and the value of harmonic constant of D2O. I am really in very serious trouble. Udaya Raj Dahal Tribhuwan University Nepal ________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. <https://signup.live.com/signup.aspx?id=60969>
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