[gmx-users] PMF

[Alex]

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 !?

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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