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 !?
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
>> but no success unfurtunatly.
>> For some force constant the peptide would not desorbed from the surface
>> 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?
> 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
>> in each step below, I would be so appreciated if you could guide me to
>> improve the results?
>> PMF result:
> 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.
> Force in pulling SMD
>> position in pulling SMD
>> Thank you very much in advance.
> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.