[gmx-users] Heme topology

We have a heme for which PRODRG does not generate the topology file, as Fe atom is not supported. Is there an alternative for generating topology file for Heme molecule? Thanks and Regards, Raghu -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Dihedral parameters from QM and MM relaxed surface scans

On 4/29/18 7:16 PM, Eric Smoll wrote: Justin, I see. Unless there are other problems impacting my observations (e.g, a need for double-precision GROMACS for energy minimization, some sort of QM-software dependent implementation of the QM method, etc.), the QM dihedral PES does not match the

Re: [gmx-users] Dihedral parameters from QM and MM relaxed surface scans

Justin, I see. Unless there are other problems impacting my observations (e.g, a need for double-precision GROMACS for energy minimization, some sort of QM-software dependent implementation of the QM method, etc.), the QM dihedral PES does not match the unrestrained MM PES from the literature.

Re: [gmx-users] Dihedral parameters from QM and MM relaxed surface scans

On 4/29/18 5:48 PM, Eric Smoll wrote: Mark, *Thank you for the reply! * I understand your conclusion but I am trying to rule out workflow errors on my part before I make decisions based on the suitability of this forcefield. Let's say I am testing a QM-geometry optimized molecule with two

Re: [gmx-users] Dihedral parameters from QM and MM relaxed surface scans

Mark, *Thank you for the reply! * I understand your conclusion but I am trying to rule out workflow errors on my part before I make decisions based on the suitability of this forcefield. Let's say I am testing a QM-geometry optimized molecule with two identical (same parameters) and coupled

Re: [gmx-users] Dihedral parameters from QM and MM relaxed surface scans

Hi, Your two PES scans are over the same coordinates, and by construction you are balancing the normal FF contributions against an intended-as-strong restraint. The only thing that is different between your two sets of PE calculation is the contribution of the restraint. If the normal FF was

Re: [gmx-users] Force fields

Hi, Posting just before a weekend isn't all that likely to get a quick reply... ;-) Note that your 2, 3, and 4 have Si-O-Si angles (and related dihedrals) which isn't found in 1, so you clearly cannot take the parameters for 1 and construct a complete topology for 2, 3, and 4. So you still have

[gmx-users] structure factor

Hi, Is there a way to calculate structure factor in gromacs? From the gmx rdf function? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Force fields

Any idea, please? Cheers, Alex On Fri, Apr 27, 2018 at 5:50 PM, Alex wrote: > Dear all, > I have the Gromos-54A7 force fields (FF) for the molecule number 1 in the > below link, using thoes how I can have the FF for the molecules number 2,3 > and 4 in the same link