[gmx-users] Gromacs 5 umbrella sampling

[Andres Ortega Guerrero]

Thank so much Justin for the help, 
I am going to reinstall gromacs 5 and try, I decided to install gromacs 4.6.5, and instead of a flat  bottom potential , uses position restraint in x and y , in order to get the pmf of a drug passing throughout of an ion channel , I don't know if this could affect that much due to this bias(do you think so?) , but If I have time try to get both using gromacs 5 , 

Thanks again 

Andrés Ortega 
Ing. Electrónica 
Universidad del Valle 

El 7/04/2014, a las 20:45, "Justin Lemkul" <jalemkul at vt.edu> escribió:

> 
> 
> On 4/4/14, 10:48 AM, Andres Ortega Guerrero wrote:
>> Thank you Justin,
>> 
>> I will appreciate the help with this doubt, of the reference group, that is not 0 , is 26 in the index file,
>> or the appropiate definition of the reference group thanks
> 
> I want to revisit this because I am now working through it myself.  What was not immediately clear is that these indices do not, in fact, have anything to do with the order of the index file.  Instead, the indices correspond to the groups used in pulling.
> 
> Since the pull code is now more general, such that multiple reaction coordinates can now be defined (and thus more than one reference group), one must specify the number of reaction coordinates (pull-ncoords), how many groups total are involved in any sort of reaction coordinate (pull-ngroups), and then identify which of those groups are participating in each of the reaction coordinates.
> 
> The simplest case is to use the biasing potential along one reaction coordinate with two groups.  Therefore:
> 
> pull-ngroups = 2
> pull-ncoords = 1
> pull-coord1-groups = 1 2
> pull-group1-name = refgroup
> pull-group2-name = pullgroup
> 
> I have that much working at this point.  One could, in theory, then extend the situation to have two reaction coordinates between 3 or 4 groups, i.e.
> 
> pull-ngroups = 3
> pull-ncoords = 2
> pull-coord1-groups = 1 2
> pull-coord2-groups = 1 3
> pull-group1-name = refgroup
> pull-group2-name = pullgroup1
> pull-group3-name = pullgroup2
> 
> I assume that will work (famous last words, but I have no time or need to test that setup at the moment).  What it is intended to do is apply a biasing potential between groups 1 and 2, and 1 and 3 simultaneously.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
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