[gmx-users] Freezing part of the molecules!!!
ababakha at mccammon.ucsd.edu
Fri Jun 9 00:17:17 CEST 2006
Can you use this freezegroups function during a minimizaiton? (say if
you wanted to minimize solvent around your protein, while keeping the
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 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 belong to your 1st
>> group and so on. Remember to use the numbering as it is in the
>> gro file.
>> This you can do with "make_ndx -f your_gro_file.gro"
>> 2. Add the folling to your mdp file:
>> freezegrps = Group1 Group2 Group3 Group4 Group5
>> freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
>> Note that for each group defined as freezegroup you need to
>> specify the
>> dimensions that you want to freeze (x y z). This is done with either
>> Y or N. So if you want only to freeze Group1 in the z-direction
>> you write:
>> freezegrps = Group1
>> freezedim = N N Y
>> All the best,
> Just as a warning: please note that combining:
> constraints + freeze groups + pressure coupling
> will give undefined results.
>> Quoting Marcelo Fabricio Masman <mmasman at gmail.com>:
>>> 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. For
>>> my protein group has 5 protein chains with 42 residues each of them.
>>> I would
>>> like to freeze (in all directions) the alfa Carbon atoms for
>>> residues 18-42
>>> for each chain. Does somebody know if it is possible to do such
>>> thing with
>>> GROMACS? Can somebody help me?
>>> Thanks a lot, in advance
>> This mail sent through IMP: http://horde.org/imp/
>> gmx-users mailing list gmx-users at gromacs.org
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users