[gmx-users] PMF

[Justin Lemkul]

On 10/13/16 5:28 AM, Alex wrote:
> Thanks for your response.
>
> Actually I fully followed your tutorial. the pull-coord1-rate = 0.007
> indicated in the pdf file is just for the pulling step and then in the next
> step I have  pull-coord1-rate = 0.0 for each windows. Can we do the pulling
> step with pull-coord1-rate = 0.0 !?
>

No, that would accomplish nothing.  To cause a net displacement, you must have a 
non-zero pulling rate.  To do umbrella sampling, you need a zero pulling rate.

Your histograms indicate that you have sampling at both positive and negative 
values along the reaction coordinate.  For a simple pull away from a surface, 
there should be no sign change.  So you have some sort of artificial behavior, 
e.g. jump across a periodic boundary, that is throwing off your whole PMF.

-Justin

> Regards,
> Alex
>
> On Thu, Oct 13, 2016 at 12:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/11/16 4:01 PM, Alex wrote:
>>
>>> Dear gromacs user,
>>>
>>> I am trying to simulate the PMF a small peptide adsorbed to a solid
>>> surface
>>> but no success unfurtunatly.
>>> For some force constant the peptide would not desorbed from the surface
>>> and
>>> for higher force constants what you can see in enclosed file will happen.
>>> Some question is:
>>> If it is possible to somehow change the force constant for a coordinate
>>> while pulling step? for example the first 1 ns by by k1 = 5000 and then
>>> reduced to k1 = 1000 for the rest of pulling.
>>>
>>>
>> gmx wham won't account for changes in k over time.  But you can use
>> different force constants in different windows; that's fine.
>>
>> Also, the force constant in the pulling step and umbrella sampling do not
>>> need to be the same necessarily?
>>>
>>>
>> Correct.
>>
>> How I can improve or increase the number of sampled frame?
>>>
>>>  I have enclosed some results as well as mdp file and force in pulling
>>> step
>>> in each step below, I would be so appreciated if you could guide me to
>>> improve the results?
>>>
>>> PMF result:
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDMC1Ua3BWLUZ3XzA
>>>
>>>
>> If you have a non-zero pulling rate (which you have specified above),
>> you're not doing umbrella sampling, you're doing non-equilibrium SMD.  So
>> this PMF is junk.  You need to have multiple windows, each with a set
>> reference restraint distance, and a zero pull rate so the conformations can
>> oscillate about that reference length.
>>
>> -Justin
>>
>> Force in pulling SMD
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDVWxkd2VLUmozUjg
>>>
>>> position in pulling SMD
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDa0VKX0E0Zlp1ODA
>>>
>>> Windows-com
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDR0poVlM2RTVSNG8
>>>
>>> md-production.mdp
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDdGFRbWQzb29Nbmc
>>>
>>> md-pulling.mdp
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDc2NPdlVmSmwydFk
>>>
>>> nvt-umbrella.mdp
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDSk9LS2d2Q1pTN2s
>>>
>>> npt-umbrella.mdp
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDVnB4STFxeENfREU
>>>
>>> md-umbrella.mdp
>>> https://drive.google.com/open?id=0B_CbyhnbKqQDQmFTZWRkR1BkcUE
>>>
>>> Thank you very much in advance.
>>>
>>> Regards,
>>> Alex
>>>
>>>
>> --
>> ==================================================
>>
>> 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

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