Re: [gmx-users] Freezing part of the molecules!!!

Arneh Babakhani wrote: Can you use this freezegroups function during a minimizaiton? (say if you wanted to minimize solvent around your protein, while keeping the protein fixed?) please try before you buy, sorry before asking questions... this should work anyway. David van der Spoel wrote:

Re: [gmx-users] Freezing part of the molecules!!!

Can you use this freezegroups function during a minimizaiton? (say if you wanted to minimize solvent around your protein, while keeping the protein fixed?) David van der Spoel wrote: Soren Enemark wrote: Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups t

Re: [gmx-users] Freezing part of the molecules!!!

Soren Enemark wrote: Quoting David van der Spoel <[EMAIL PROTECTED]>: Soren Enemark wrote: Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups that you want to freeze. Such an index file should look like: [ Group1 ] 45 46 47 48 49 ... [ Group2 ]

Re: [gmx-users] Freezing part of the molecules!!!

Quoting David van der Spoel <[EMAIL PROTECTED]>: > Soren Enemark wrote: > > Hi Marcelo, > > what you need to do is: > > > > 1. create an index file (.ndx) with the groups that you want to freeze. > > Such an index file should look like: > > [ Group1 ] > > 45 46 47 48 49 ... > >

Re: [gmx-users] Freezing part of the molecules!!!

Soren Enemark wrote: Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups that you want to freeze. Such an index file should look like: [ Group1 ] 45 46 47 48 49 ... [ Group2 ] 106 107 ... [ Group3 ] where atoms number 45, 46

Re: [gmx-users] Freezing part of the molecules!!!

Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups that you want to freeze. Such an index file should look like: [ Group1 ] 45 46 47 48 49 ... [ Group2 ] 106 107 ... [ Group3 ] where atoms number 45, 46, 47, 48, and 49 etc be

Re: [gmx-users] Freezing part of the molecules!!!

Hi!just make an index file (make_ndx) custom-defining the groups which you need to freeze, in your case the C-alpha of residues 18-42. Remember that, when you define new groups, you should delete the corresponding atoms from the group that contains all the rest of the protein atoms, if not you'll g

[gmx-users] Freezing part of the molecules!!!

Hi all!!!   I am trying to run a MD simulation with part of my system frozen. I was looking into the manual but I couldn't find the answer since the manual says the way for freezing complete groups. I would like to freeze only a part of my protein and permit the completed optimization of the rest.