[gmx-users] (no subject)

He, Yang yang.he at mavs.uta.edu
Mon Apr 20 03:09:10 CEST 2009 

Hi Justin,

My version is a little old just 3.3.1 and I work in the LINUX system . As for my system, I have four single CG DNA model put in the box  randomly to see whether they can hybridize with the matched single strand while I need to keep the two strand fixed through fixing one or two atoms in that single strand .  Hence, I use the position restraints to fix the two atoms in one single strand .

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 5:28 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)

He, Yang wrote:
> Hi Justin,
>
> In fact, I have tried to use freezegrps to freeze a whole single CG DNA strand  and it works but if I want to freeze some atoms in this single strand, it seems that I have no choice but choose the position restraints. The freezegrps seems not to work for that. But the error  for the position restraints always is fragmentation fault and can not be fixed although many methods have been tried.
>

So then the following is true:

freezegrps = DNA works fine
freezegrps = (your groups) gives "Invalid order for directive defaults"

That would make no sense.  The error comes from the topology, not anything
specified in the .mdp file, so I don't understand.

> I don't know whether this is a bug in the gromacs cause I have followed the steps in manual to simulate a case(about speptide) in manual with position restraints while it still doesn't work. I am confused about that.
>

I doubt it is a bug; this would be pretty prohibitory for most users.  It may be
specific to your system.  If you can provide details of your system, compilers,
which Gromacs version you are using (provided in a new thread that has a
noticeable subject line), you may be able to sort that issue out.

-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 4:41 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] (no subject)
>
> 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
>>>> _______________________________________________
>>>> 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!
>>>> 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
>>>>
>>> --
>>> ========================================
>>>
>>> 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!
>>> 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
>>>
>> --
>> ========================================
>>
>> 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!
>> 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
>>
>
> --
> ========================================
>
> 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!
> 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
>

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

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!
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 mailing list