[gmx-users] Re: PMF of ligand transport

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Aswathy wrote:
>> Hi Justin,
>>
>> I am sorry, i dint understand this point "Your problem was only 
>> related to the actual umbrella sampling itself." ? You meant I just 
>> want to repeat umbrella sampling only?
>>
> 
> Yes.  The manner in which you generate the initial configurations on 
> which you will conduct umbrella sampling is quite irrelevant.
> 
>> In order to further understand that "Distance " problem, May I ask one 
>> more question,( please ignore if its a stupid one..)
>> As Thomas suggested, = is the channel and x the dummy and l the ligand
>> x l =====
>> later time
>> x   ==l==
>> If this is the case, then  there wont be sign problem with "distance", 
>> right???  (Once again forgive me if I am wrong, because I know you 
>> already put your maximum effort to make me understand this thing)
>>
>>  And if we use a dummy particle, will the movement  of that particle 
>> will also matter ? How can we fix that?
>>  
> 
> I think this is a rather complicated approach and you will probably 
> spend a lot of unnecessary time troubleshooting it.  It might work, but 
> you don't need it. Your problem is not with the SMD portion of the 
> protocol.  Your problem is with umbrella sampling, which is a separate 
> concept.

I think I mis-read Thomas' post, but I'll agree with Chris that this approach is 
still rather complicated and potentially error-prone.  Using the appropriate 
pull_geometry and a sensible reference group during umbrella sampling is all you 
need to do.

-Justin

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

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

========================================