[gmx-users] Constraint distance question

Hi, I am trying to look at the free energy differences as a function of end-to-end distance of peptides in water. I am running a set of simulations with the two atoms of interest joined by a type 2 constraint, with the length varying from 0.5 to 3 nm. However, these simulations all ex

Re: [gmx-users] constraint distance between ligand and protein

Kanin, On 9/11/06, kanin wichapong <[EMAIL PROTECTED]> wrote: Hi All, I would like to know how to make a distance constraint between the ligand and the protein. If I just merge two chain together by pdb2gmx, it can done if the two chain are both protein. However, if it is a ligand and protei

Re: Re: SV: Re: [gmx-users] constraint distance

Allow me to take this opportunity to reiterate that the ability to only apply distance/angle/dihedral restraints between atoms in the same "molecule" (in the topology sense) is really lame. It would be really nice if GROMACS could handle absolute atom numbering for restraints (i.e. using the numbe

[gmx-users] constraint distance between ligand and protein

Hi All,    I would like to know how to make a distance constraint between the ligand and the protein. If I just merge two chain together by pdb2gmx, it can done if the two chain are both protein. However, if it is a ligand and protein, i can't merge together because there is no libraly for the liga

SV: Re: SV: Re: [gmx-users] constraint distance

David van der Spoel <[EMAIL PROTECTED]> skrev: Soren Enemark wrote:> Hi,> maybe I am misunderstanding either the manual or the topic.. but - in > my world -> I never stop being puzzled by the part of chapt 6 in the manual which > apparently> says that such distance constraining is possible even

Re: SV: Re: [gmx-users] constraint distance

> Hi, > maybe I am misunderstanding either the manual or the topic.. but - in my > world - > I never stop being puzzled by the part of chapt 6 in the manual which > apparently > says that such distance constraining is possible even though it (seems) > to be > secretly known that it is _not

Re: SV: Re: [gmx-users] constraint distance

Soren Enemark wrote: Hi, maybe I am misunderstanding either the manual or the topic.. but - in my world - I never stop being puzzled by the part of chapt 6 in the manual which apparently says that such distance constraining is possible even though it (seems) to be secretly known that it i

SV: Re: [gmx-users] constraint distance

 Hi,  maybe I am misunderstanding either the manual or the topic.. but - in my world -  I never stop being puzzled by the part of chapt 6 in the manual which apparently  says that such distance constraining is possible even though it (seems) to be  secretly known that it is _not_ possible unless on

Re: [gmx-users] constraint distance

Hi Kanin, The only way to get away with that is to merge your two parts to form one molecule, with the only connection being a distance_restraint (or another bonded term if you want to emulate bond-like behaviour such as a salt-bridge). Best, Tsjerk On 9/11/06, kanin wichapong <[EMAIL PROTECTE

[gmx-users] constraint distance

Dear All    I would like to know how to constraint the distance between the different molecule, ex. the ligand and the protein. As far as I know whatever to do the constraint, distance, angle dihedral, it can do just in the same molecule.     Thank you in advance for all of your help.With B