[gmx-users] (no subject)

[He, Yang]

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?

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

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