[gmx-users] snap shot

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> 
> How can I save the coordinates  (in pdb or xyz format) for a particular
> snap shot.
> 

trjconv -dump

-Justin

> Nilesh
> 
> On Sat, October 8, 2011 10:06 am, lina wrote:
>> On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal
>> <ndhumal at andrew.cmu.edu>wrote:
>>
>>
>>> Hello,
>>>
>>>
>>> I have a system with 128 emi (cations) and 128 Cl (anions). I run the
>>> simulation for 20 ns.
>>>
>>> I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.
>>>
>>>
>> trjconv  use -dt 5000
>>
>>> I don't want to save snap shot for 128 ion-pairs. How can I take
>>> average over 128 ion pairs and save snap shot for a single ion pair.
>>>
>> I don't understand the average mean here?
>> if you wanna get the average.pdb in some time interval try g_rmsf -ox  -b
>> -e
>>
>>
>> you may wait for some other better answers.
>>
>>
>>> Basically I want to use classical md geometry for quatum chemical
>>> calculation.
>>>
>>> I am using Gromacs 4.0.7 version.
>>>
>>>
>>> Thanks
>>>
>>>
>>> Nilesh
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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