it still isn't clear what you want to do. why use umbrella sampling for
this, instead of TI or FEP?
On Wed, Mar 9, 2011 at 1:55 PM, Rajesh Raju
<rajesh.raju.mail.chem.tamu.edu>wrote:
> Dear Carlos,
>
> Thank you very much for your reply. I have attached the receptor molecule
> structure with this email. I would like to studnt binding free energy of
> small solutes like benzene. I have shown the reaction coordinate. I want to
> generate aPMF profile for the inclusion of the solute molecules into this
> receptor. I can do the umbrella sampling in two different ways. One way is
> to make the coordinate and tolopoly files for different distance restraint
> and do umbrella sampling. The advantage is the dist_vs_time value will start
> from the closet value correspond to the distant constraint value. Second way
> is to keep the solute and receptor molecules at same configuration and do
> individual simulations corresponding to the different distance constraint
> value. Would both give the same PMF profile ? If different why and which is
> the best approach?
>
> Thanking you in advance
> Rajesh
>
>
>
>
> On Wed, 9 Mar 2011 07:04:24 -0500
> Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
>> you haven't made it clear what you're trying to calculate. Are you
>> following
>> a procedure shown to work well in a peer-reviewed article? I suspect that
>> what you want to do is quite challenging. Keep in mind that umbrella
>> sampling works well ONLY if the reaction coordinate you choose is the one
>> responsible for the relevant energy changes, and you must be able to fully
>> sample over motions in all of the other degrees of freedom in each of the
>> umbrella windows. I suspect that at a fixed distance you will find it
>> difficult to properly sample over all other motions (such as side chains,
>> ligand flexibility, etc.
>>
>> given that, I'm not sure quite what you're asking. It seems that you have
>> different numbers of waters. you can adjust the water buffer length in
>> leap
>> when you build the molecule- it might require trial and error.
>>
>> during your umbrella runs, make sure that you have overlap in the
>> distribution of distances (histogram them) between all neighboring
>> windows.
>> any gaps will result in errors in free energy profile.
>>
>>
>>
>> On Tue, Mar 8, 2011 at 6:21 PM, Rajesh Raju
>> <rajesh.raju.mail.chem.tamu.edu>wrote:
>>
>> Dear Amber users,
>>>
>>> I am planning to do an umbrella sampling on one of the receptor
>>> molecule. I used the distance between the center of masses of the
>>> receptor and ligand molecule as constraint. My doubts are:
>>>
>>> [1] Do I need to make different coordinate files for the complex,
>>> corresponding to the distance between the center of masses of the two
>>> molecules? or Can I use the same coordinate file for all individual
>>> simulations of the different windows?
>>>
>>> [2] changing the distance variable in the 'DISANG=dist.dat' file to
>>> different distance values corresponding to different windows, and keep
>>> the same coordinate files with center of masses of two molecules close
>>> to zero, would be the same effect as that of the doing different
>>> window simulations, making new coord files corresponding to the
>>> umbrella sampling distance.
>>>
>>> So far I proceeded with the second approach:
>>>
>>> I made the new coordinates corresponding to different R variables from
>>> 0.5 to 10 ..20 windows. and made parameter and coordinate files for
>>> the individual windows..The number of water molecules are slightly
>>> different....
>>>
>>> Which is the best way?
>>>
>>> Thanks
>>> Rajesh
>>>
>>> _______________________________________________
>>> 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
>>
>
>
> _______________________________________________
> 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
Received on Thu Mar 10 2011 - 07:00:04 PST
