[gmx-users] PMF

[Alex]

The negative and positive in the the reaction coordinate comes probably
from interaction of peptide with surface in bottom slab and top(next cell
beacuse of PBC) slab in the Z direction.
But I was always taking care about sampled windows so that the peptide
pulled away from top of bottom surface to the midd point of box out of cut
of and all the sampled windows was chosen from the bottom part of the box.,
and this means no interaction it should have with the top slab in the next
cell.

-----------------------      ----> top slab



            ----                  ----> midd of box
                            }
                            }     -----> 39 Sampled windows
                            }
-----------------------      ----> Bottom slab


Regards,
Alex

On Thu, Oct 13, 2016 at 2:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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