Re: [gmx-users] Photodissociation through MD

2012-09-21 Thread francesco oteri
Hi, could you try to use the Morse potential for this bond. As far as I know, the parameters can be directly obatined forml the armonic potential expression. Francesco 2012/9/21 Mark Abraham > On 21/09/2012 11:35 AM, Rajiv Gandhi wrote: > >> Dear all gromacs users, >> >> In myoglobin system, ho

Re: [gmx-users] Photodissociation through MD

2012-09-20 Thread Mark Abraham
On 21/09/2012 11:35 AM, Rajiv Gandhi wrote: Dear all gromacs users, In myoglobin system, how we can cut the bond between Fe-C to produce the photodissociation through MD?. By not making it in your topology. Whatever procedure you follow for making the other Fe-C interactions needs to differ f

Re: [gmx-users] Photodissociation through MD

2012-09-20 Thread Justin Lemkul
On 9/20/12 9:35 PM, Rajiv Gandhi wrote: Dear all gromacs users, In myoglobin system, how we can cut the bond between Fe-C to produce the photodissociation through MD?. I have seen there are number of studies over photodissociation and also I believe that people have used their appropriate par