[gmx-users] (no subject)

[Justin A. Lemkul]

He, Yang wrote:
> It always show the common error  "Invalid order for directive defaults".I suppose it is because I have  defined an atom belonging to two groups . What do you mean "by freezing subgroups of atoms
> within a molecule" ? I just wonder how to make it ?Can you give me some examples?
> 

The error is unrelated to your freezegrps.  See here:

http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults

Your index groups should be fine.  A "subgroup" refers to select atoms within a 
molecule, as in backbone of the protein, headgroups of lipids, or some such 
similar idea.  As I said before, your use of freezegrps and index groups should, 
in theory, be fine.

-Justin

> Thank you very much.
> 
> Yang
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Sunday, April 19, 2009 3:47 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] (no subject)
> 
> He, Yang wrote:
>> Hi Justin,
>>
>> In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group.
>>
> 
> Alright, so what's the error?  You should be able to freeze subgroups of atoms
> within a molecule; I've done it several times in different instances.
> 
> -Justin
> 
>> Yang
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
>> Sent: Sunday, April 19, 2009 1:42 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] (no subject)
>>
>> He, Yang wrote:
>>> Hi all users,
>>>
>>> I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this:
>>>
>>> [God]
>>> 21  22
>>> [Bad]
>>> 61  62
>>>
>>> And  I have defined the atom numbering 21, 22, 61,62 in gro file like this :
>>>
>>> 2MOM   bT   21     0.805      1.330      3.914
>>> 2MOM   bT   22     0.448      1.572      3.576
>>>
>>>  4ICE   bT   61     0.805      4.330      3.914
>>>  4ICE   bT   62     0.448      4.572      3.576
>>>
>>> I know this may cause error cause I just define one atoms in two groups.   I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs .
>>>
>> Are you assuming an error, or have you tried it and actually received an error?
>>   Use these groups as the "freezegrps" in the .mdp file and try it.  It should
>> be fine.
>>
>> -Justin
>>
>>> I hope what  I said is clear to you all and I really appreciate your any suggestions.
>>>
>>> Yang
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 
> --
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================