[gmx-users] Distance restraints

[Justin Lemkul]

On 5/21/13 12:53 PM, Rama Krishna Koppisetti wrote:
> Hi..,Mark
>
> but it is within the same molecule , not in inter-molecules.
>

That's what distance restraints are designed for.  Please refer to the manual 
for topology syntax and explanation of the relevant parameters.

-Justin

>
>
>
> On Tue, May 21, 2013 at 11:36 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> Yes. Check out the manual first!
>>
>> Mark
>>
>>
>> On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti <
>> ramkishna72 at gmail.com> wrote:
>>
>>> Hi Mark,
>>>
>>> Is there anyway to define NMR distance restraints in MD simulations to do
>>> refinement for the complex structure.
>>>
>>>
>>>
>>>
>>>
>>> On Tue, May 21, 2013 at 10:11 AM, Mark Abraham <mark.j.abraham at gmail.com
>>>> wrote:
>>>
>>>> You can't - the atoms must be part of the same [moleculetype]. The good
>>>> news is that a [moleculetype] can have whatever you want in it, so you
>>> can
>>>> have more than one molecule. The bad news is that you'll have to be
>>> cunning
>>>> with renumbering atoms in the merged [moleculetype] and there's no
>> tools
>>>> that do that. (Or maybe there's a smart-alec trick using the pull code,
>>> but
>>>> I have no idea what.)
>>>>
>>>> Mark
>>>>
>>>>
>>>> On Tue, May 21, 2013 at 4:20 PM, Rama <ramkishna72 at gmail.com> wrote:
>>>>
>>>>>
>>>>> Dear Gromacs users,
>>>>>
>>>>> How to define distance restraints between two molecules(protein and a
>>>>> lipid)
>>>>> in a topology file.
>>>>>
>>>>>
>>>>> Thanks..
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> View this message in context:
>>>>> http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html
>>>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>>>> --
>>>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>>>>
>>>> --
>>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>>>
>>> --
>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>>
>> --
>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>

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

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

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