Re: [gmx-users] Help with defining new residue (OXY--HEME)

defining new residue (OXY--HEME) To: "Discussion list for GROMACS users" Date: Monday, June 21, 2010, 9:02 AM Omololu Akin-Ojo wrote: > Hi, > > I obtained parameters for a Morse potential between Oxygen molecule and Iron > in heme (from ab initio calculations).  How ca

[gmx-users] Help with defining new residue (OXY--HEME)

Hi, I obtained parameters for a Morse potential between Oxygen molecule and Iron in heme (from ab initio calculations).  How can I use this potential with the GROMOS96 parameters? I thought of a couple of options: 1) Define a new residue -- OXYHEM using the same parameters for HEME as in ffG4

Re: [gmx-users] Determining types for GROMOS96 force field

Akin-Ojo wrote: > Hi, > > With the GROMOS96 force field, how do I know what atom types I need to > include in my input > files [e.g., for Carbon(sp3) interacting with another Carbon(sp2), which of > the parameters for Carbon should I use?]. Is there some quickly accessible

[gmx-users] Determining types for GROMOS96 force field

Hi, With the GROMOS96 force field, how do I know what atom types I need to include in my input files [e.g., for Carbon(sp3) interacting with another Carbon(sp2), which of the parameters for Carbon should I use?]. Is there some quickly accessible article/document containing this information? Th

Re: [gmx-users] Virial from non-bonded forces

. Thanks for your time! o. From: David van der Spoel To: Discussion list for GROMACS users Sent: Tuesday, February 10, 2009 12:52:06 PM Subject: Re: [gmx-users] Virial from non-bonded forces Omololu Akin-Ojo wrote: > Hi, > I have two main issues: &g

[gmx-users] Virial from non-bonded forces

Hi,   I have two main issues:   1. In Appendix B of the GROMACS user manual, there is a discussion of the calculation of the virial. The top of the second page of the appendix (just before B.1.2) states, "In a triclinic system there are 27 possible images of i, ...". My question is: In this case

Re: [gmx-users] GROMACS & Speed

Thanks, David. i appreciate your response.o.David van der Spoel <[EMAIL PROTECTED]> wrote: Omololu Akin-Ojo wrote:> Hi,> > i use GROMACS & i like it because it is so fast. But, i would like to > know if GROMACS "cut corners" ? Otherwise, why is it is so fast?> i

[gmx-users] GROMACS & Speed

Hi,i use GROMACS & i like it because it is so fast. But, i would like to know if GROMACS "cut corners" ? Otherwise, why is it is so fast?if you have a fortran compiler on an Opteron box, GROMACS does not use the assembly loops. Right? So, why is it blazingly fast?o. Sponsored Link Try Netflix to