[gmx-users] Restrained Molecule is Moving

[Jennifer Casey]

Thank you so much for your quick response.

I have attached my .itp, and .top files.  I think that the if statement was
originally in the wrong spot, but after changing in and running an energy
minimization, there is still some drifting - the Na+ moves to (0.566, 1.559,
1.586) from (0.486, 1.621, 1.621).  Maybe this is normal amount of drift?

Thanks again,
Jenny

On Tue, Feb 2, 2010 at 6:01 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jennifer Casey wrote:
>
>> Hello,
>>
>> I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620)
>> of my box of dimensions 3.2418 X 3.2418 X 3.2418 nm.  The box is also full
>> of 253 THF molecules.  I added the following to the bottom of my .itp file:
>>
>> #ifdef POSRES
>> #include "posre_Na+.itp"
>> #endif
>>
>> I wrote the posre_Na+.itp file myself, it just includes the position
>> restraints for Na+, which is atom 1 in my .gro file, and my posre_Na+.itp
>> file deals with atom 1.  The force constants are all 1000.
>>
>>
> It does not matter so much whether the atom number is the same, but rather
> if the position restraint definition directly follows the [moleculetype]
> definition of Na+ in your system.  Without seeing your topology file,
> there's no way to know if you've placed the position restraint file in the
> right place.
>
> -Justin
>
>
>  Under the .mdp file, I also made sure that define = -DPOSRES.
>>
>> I get no errors when things run, but I do get my Na+ moving around.  After
>> I do energy minimization, Na+ ends up at the position (0.373, 1.504, 1.226).
>>  I also do not notice anything about position restraints appearing in my
>> .log file afterwards.
>>
>> I really appreciate the help.
>>
>> Thank you,
>> Jenny
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100202/088e6aa2/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: thf-NaI.itp
Type: application/octet-stream
Size: 1897 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100202/088e6aa2/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: thf-NaI.top
Type: application/octet-stream
Size: 134 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100202/088e6aa2/attachment-0001.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: posre_Na+.itp
Type: application/octet-stream
Size: 154 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100202/088e6aa2/attachment-0002.obj>