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 <jalem...@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

jalem...@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

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

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