Hi,
Maybe RAMD (Random Acceleration Molecular Dynamics) is an other possibility:
http://projects.eml.org/mcm/software/namd/
HTH,
Balazs
Jason Swails wrote:
> On Tue, Aug 17, 2010 at 12:04 PM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
>
>
>> Catherine,
>> It seems like these are more general science questions not related
>> directly to "how to use AMBER" but If you are
>> trying to identify pathways, the first method I would recommend that AMBER
>> has to offer is nudged elastic band (NEB). Which is specifically designed
>> to
>> find pathways. The methods Jason mentioned are used primarily to calculate
>> PMF once an ideal pathway has
>> been found. I would recommend reading the many articles referenced in the
>> AMBER manual regarding "NEB".
>>
>>
>
> I threw NEB in there at the end :). However, as I understand it, NEB won't
> really give a PMF in the sense that it won't be a free energy path along
> that coordinate. I think you need to further use umbrella sampling at
> various points along that coordinate in order to actually generate the PMF
> after the NEB simulation. Am I right?
>
> All the best,
> Jason
>
>
>
>> However, if it is a relatively simple pathway, of course PMF methods are
>> the
>> way to go.
>>
>> --Dan
>>
>> On Wed, Aug 18, 2010 at 12:36 AM, Catein Catherine
>> <askamber23.hotmail.com>wrote:
>>
>>
>>> Thank you Jason,
>>>
>>>
>>>
>>> How about if I was doing this with umbrella sampling?
>>>
>>>
>>>
>>> Can I identify the most important drug dissociation pathway using
>>>
>> umbrella
>>
>>> sampling? When I find different results since I used different atoms to
>>> define the distance restraint?
>>>
>>>
>>>
>>> Best regards with thanks,
>>>
>>>
>>>
>>> Catherine.
>>>
>>>
>>>> Date: Tue, 17 Aug 2010 08:56:29 -0400
>>>> From: jason.swails.gmail.com
>>>> To: amber.ambermd.org
>>>> Subject: Re: [AMBER] How to find the most important drug dissociation
>>>>
>>> pathway theoretically? PMF?
>>>
>>>> Hello,
>>>>
>>>> How are you constructing the PMF? Are you using SMD and calculating the
>>>>
>>> PMF
>>>
>>>> with the Jarzynski equation? Are you using umbrella sampling? If you
>>>>
>> are
>>
>>>> using SMD with Jarzynski averaging, you should include every single
>>>> trajectory in your average to get the total PMF. You can find likely
>>>>
>> the
>>
>>>> "best" pathway, or the one that corresponds closest to the PMF, by
>>>>
>>> comparing
>>>
>>>> the potential energy surface of each simulation with the average PMF
>>>> obtained from averaging all of them, and whichever one follows that
>>>>
>> curve
>>
>>>> closest will probably be a good choice.
>>>>
>>>> Hope this helps,
>>>> Jason
>>>>
>>>> On Tue, Aug 17, 2010 at 7:00 AM, Catein Catherine <
>>>>
>>> askamber23.hotmail.com>wrote:
>>>
>>>>> Dear All,
>>>>>
>>>>>
>>>>>
>>>>> I would like to stuy the drug dissociation pathway from a receptor.
>>>>>
>>>>>
>>>>>
>>>>> I tried to use PMF to discript the distance between the drug and the
>>>>>
>>> active
>>>
>>>>> site. I noted that the path is sensitive to the atoms used to define
>>>>>
>>> the
>>>
>>>>> distance restraint.
>>>>>
>>>>>
>>>>>
>>>>> If I want to chose the most important drug dissociation pathway for
>>>>>
>>> further
>>>
>>>>> discussion, is the one with the lowestest energy should be used? If
>>>>>
>>> not,
>>>
>>>>> what is the requirement should be used to chose the right pathway?
>>>>>
>>>>>
>>>>>
>>>>> best regards,
>>>>>
>>>>>
>>>>>
>>>>> Cat
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>>
>>>> --
>>>> Jason M. Swails
>>>> Quantum Theory Project,
>>>> University of Florida
>>>> Ph.D. Graduate Student
>>>> 352-392-4032
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>> --
>> Dr. Daniel J. Sindhikara
>> Institute for Molecular Science
>> E-mail: sindhikara.gmail.com
>> Website: http://sites.google.com/site/dansindhikara/
>> --
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
>
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Received on Tue Aug 17 2010 - 13:00:03 PDT
