Re: [gmx-users] intermolecular H bond selection

[Erik Marklund]

21 maj 2012 kl. 06.54 skrev Anirban:

> 
> 
> On Mon, May 21, 2012 at 3:09 AM, mu xiaojia  wrote:
> Thanks for prompt answering but I may need to clarify my question and sorry 
> for the understanding,
> 
> For example, I have dipeptides like Ala-Ala, how to ask g_hbond only 
> calculate the h bonds between Ala on different dipeptides instead of counting 
> all the possible h bonds between Ala(intermolecularly and intramolecularly)
> 
> 
> Make two groups with make_ndx that contains the residue numbers (or specific 
> atom numbers) of the ALA residues between which you want to count the H bonds 
> and then select these group numbers with g_hbond.
> 
> -Anirban

And if you have many alanines you might have to call g_hbond many times (think 
in the lines of scripting). Or invoke g_hbond once with the index group 
consisting of all alanines chosen twice and decompose the hbonding matrix (-hbm 
-hbn) yourself (python/perl).

Best,

Erik

>  
> Thanks very  much!
> 
> 
> On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul  wrote:
> 
> 
> On 5/18/12 7:22 PM, mu xiaojia wrote:
> Hi gmx-users,
> 
> I have a question might be explained before but I cannot understand from the
> previous , how to calculation the intermolecular h-bonds between two 
> molecules?
> I saw someone mentioned using a second tpr file, but how to do it 
> specifically?
> Thanks very much!
> 
> 
> g_hbond asks for two index groups to be selected.  Assign each molecule to an 
> index group and select them when prompted.
> 
> -Justin
> 
> -- 
> 
> 
> 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
> 
> 
> -- 
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] intermolecular H bond selection

[Anirban]

On Mon, May 21, 2012 at 3:09 AM, mu xiaojia  wrote:

> Thanks for prompt answering but I may need to clarify my question and
> sorry for the understanding,
>
> For example, I have dipeptides like Ala-Ala, how to ask g_hbond only
> calculate the h bonds between Ala on different dipeptides instead of
> counting all the possible h bonds between Ala(intermolecularly and
> intramolecularly)
>
>
Make two groups with make_ndx that contains the residue numbers (or
specific atom numbers) of the ALA residues between which you want to count
the H bonds and then select these group numbers with g_hbond.

-Anirban


> Thanks very  much!
>
>
> On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> On 5/18/12 7:22 PM, mu xiaojia wrote:
>>
>>> Hi gmx-users,
>>>
>>> I have a question might be explained before but I cannot understand from
>>> the
>>> previous , how to calculation the intermolecular h-bonds between two
>>> molecules?
>>> I saw someone mentioned using a second tpr file, but how to do it
>>> specifically?
>>> Thanks very much!
>>>
>>>
>> g_hbond asks for two index groups to be selected.  Assign each molecule
>> to an index group and select them when prompted.
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> 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
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] intermolecular H bond selection

[mu xiaojia]

Thanks for prompt answering but I may need to clarify my question and sorry
for the understanding,

For example, I have dipeptides like Ala-Ala, how to ask g_hbond only
calculate the h bonds between Ala on different dipeptides instead of
counting all the possible h bonds between Ala(intermolecularly and
intramolecularly)

Thanks very  much!


On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul  wrote:

>
>
> On 5/18/12 7:22 PM, mu xiaojia wrote:
>
>> Hi gmx-users,
>>
>> I have a question might be explained before but I cannot understand from
>> the
>> previous , how to calculation the intermolecular h-bonds between two
>> molecules?
>> I saw someone mentioned using a second tpr file, but how to do it
>> specifically?
>> Thanks very much!
>>
>>
> g_hbond asks for two index groups to be selected.  Assign each molecule to
> an index group and select them when prompted.
>
> -Justin
>
> --
> ==**==
>
> 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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] intermolecular H bond selection

[Justin A. Lemkul]

On 5/18/12 7:22 PM, mu xiaojia wrote:

Hi gmx-users,

I have a question might be explained before but I cannot understand from the
previous , how to calculation the intermolecular h-bonds between two molecules?
I saw someone mentioned using a second tpr file, but how to do it specifically?
Thanks very much!



g_hbond asks for two index groups to be selected.  Assign each molecule to an 
index group and select them when prompted.


-Justin

--


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


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[gmx-users] intermolecular H bond selection

[mu xiaojia]

Hi gmx-users,

I have a question might be explained before but I cannot understand from
the previous , how to calculation the intermolecular h-bonds between two
molecules? I saw someone mentioned using a second tpr file, but how to do
it specifically? Thanks very much!

Ja
-- 
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