Re: [gmx-users] trajectory analysis

[Turgay Cakmak]

Thank you for your reply. I will read the manual more carefully.

2012/6/5 Justin A. Lemkul 

>
>
> On 6/5/12 4:40 AM, Turgay Cakmak wrote:
>
>>
>> Hi all,
>>
>>
>> I would like to get information about *pi-pi stacking*, *van der Waals*,
>> *electrostatic and hydrophobic interactions* for my system
>> (several-peptides in
>>
>> a box filled with water). Can Gromacs compute these interactions?
>>
>>
>> As far as I see from mailing-list, to get information on *hydrophobic
>> interactions*, g_mindist and g_sas can be used. But, they look very
>> different.
>>
>> Which one should be used?
>>
>>
> Both.  There are no Gromacs tools that magically do the analysis you're
> looking for, but combinations of available tools will.  You can use
> g_mindist with a suitable index group to find hydrophobic contacts, and
> g_sas to compute hydrophobic and polar surface area.  Other tools that can
> be useful for your other metrics are g_hbond, g_dist, and others.  See the
> manual for a complete listing and decide what might be useful based on what
> you read there.
>
> -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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Re: [gmx-users] trajectory analysis

[Justin A. Lemkul]

On 6/5/12 4:40 AM, Turgay Cakmak wrote:


Hi all,


I would like to get information about *pi-pi stacking*, *van der Waals*,
*electrostatic and hydrophobic interactions* for my system (several-peptides in
a box filled with water). Can Gromacs compute these interactions?


As far as I see from mailing-list, to get information on *hydrophobic
interactions*, g_mindist and g_sas can be used. But, they look very different.
Which one should be used?



Both.  There are no Gromacs tools that magically do the analysis you're looking 
for, but combinations of available tools will.  You can use g_mindist with a 
suitable index group to find hydrophobic contacts, and g_sas to compute 
hydrophobic and polar surface area.  Other tools that can be useful for your 
other metrics are g_hbond, g_dist, and others.  See the manual for a complete 
listing and decide what might be useful based on what you read there.


-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] trajectory analysis

[Turgay Cakmak]

Hi all,


I would like to get information about *pi-pi stacking*, *van der
Waals*, *electrostatic
and hydrophobic interactions* for my system (several-peptides in a box
filled with water). Can Gromacs compute these interactions?


As far as I see from mailing-list, to get information on *hydrophobic
interactions*, g_mindist and g_sas can be used. But, they look very
different. Which one should be used?


I would deeply appreciate your response.

My best regards,

Turgay,
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Re: [gmx-users] trajectory analysis

[Mark Abraham]

On 30/05/2012 4:45 PM, oguz gurbulak wrote:

Dear All,
I want to ask some questions about trajectory analysis. I have some md 
simulation output files that includes coordinate, force and velocity 
information. And these files are huge ( more than 5 GB ) . Could you 
please recommend a free text editor which works on Linux or Windows to 
open and editthese huge files? And I will run these files with fortran 
codes and get again huge output files . In order to do this operation 
faster and seamlessly what should I do ? Which facilities do I have on 
pc ? Could you please share your experiences with me ?




The advice of 
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume 
is applicable to managing these situations. A few minutes of thought can 
save hours of I/O processing.


Mark
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[gmx-users] trajectory analysis

[oguz gurbulak]

Dear All,
 
I want to
ask some questions about trajectory analysis. I have some md simulation output
files that includes coordinate, force and velocity information. And these files
are huge ( more than 5 GB ) . Could you please recommend a free text editor 
which
works on Linux or Windows to  open and editthese huge files? And I will run
these files with fortran codes and get again huge output files . In order to do
this operation faster and seamlessly what should I do ? Which facilities do I 
have on pc ? Could you please share
your experiences with me ?
 
Thanks for
any help.
 
Kind regards.-- 
gmx-users mailing listgmx-users@gromacs.org
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