[gmx-users] Free Energy Landscape- PCA

[Justin Lemkul]

On 12/15/16 10:02 AM, Romero, Raquel wrote:
> Thanks a lot for your reply, Justin. That’s exactly what want but my problem is that don’t know how, I mean, how can I know that correspondence? Getting that correspondence is my only problem

You (presumably) constructed a time series of eigenvalues from gmx anaeig -proj 
along PC1 and PC2, after which you constructed the free energy surface.  That 
means you have a time series of eigenvalues of those configurations projected 
onto PC1 and PC2.  So after you identify the bin in the 2-D surface that the 
configurations fall, then you have a range of values to which those 
configurations correspond.  Then you just write a little script that parses the 
PC1 and PC2 eigenvalue time series and when it identifies eigenvalues that 
simultaneously fall inside the limits, print out the time value.  Then apply 
trjconv.

-Justin

>
>
>
>
>> On 14 Dec 2016, at 12:49, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 12/12/16 9:30 AM, Romero, Raquel wrote:
>>> Hi everyone,
>>>
>>>
>>> I have a number of trajectories over which I have conducted PCA using Gromacs. I have also generated a Free Energy Landscape using g_sham when the trajectory is projected along the PCs. I would like to know how I can extract the coordinates of those states of minimum energy shown in the FEL.
>>>
>>
>> You'll need to find the corresponding frames by matching the eigenvalues from the time series.  Then you can dump out those frames using trjconv -dump.
>>
>> -Justin
>>
>>>
>>> Thanks in advance,
>>>
>>>
>>> Regards
>>>
>>>
>>>
>>> Raquel Romero
>>> Department of Pharmaceutical and Biological Chemistry
>>> UCL School of Pharmacy, University College London
>>> 29/39 Brunswick Square
>>> London
>>> WC1N 1AX
>>>
>>> T: 0207 753 5972
>>> E: raquel.romero.12 at ucl.ac.uk
>>>
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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