it more accuratly represents reality (my opinion), but is not feasable with high energy affinities such as protein-protein or DNA-protein interactions with short (under u or m seconds) and is used as such (I assume) in many things, or you cant pull them apart. A comparison however, would probably not show much difference ( a basketball with a small marble or even beebee thrown at it depending on what your looking at). I would say any published things should just maintain consistence, but trying one or two differences to see is research.
Stephan Watkins
Gesendet: Donnerstag, 08. August 2013 um 21:57 Uhr
Von: rookie417 <surampu...@gmail.com>
An: gmx-users@gromacs.org
Betreff: [gmx-users] Umbrella sampling - position restraints
Von: rookie417 <surampu...@gmail.com>
An: gmx-users@gromacs.org
Betreff: [gmx-users] Umbrella sampling - position restraints
Dear GROMACS users,
I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulations later
during analysis. The simulations ran normally and the PMF plots look
accurate. However, I realized that position restraints were not applied only
after looking at the log files and position restraints energy values were
missing. The umbrella sampling MD simulation was for 2 ns only and I checked
the pullx-umbrella.xvg files and the COM fluctuations are not that bad
considering its only a short time for convergence.
Can anyone comment on how not using position restraints would effect the
result otherwise?
Thanks
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I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulations later
during analysis. The simulations ran normally and the PMF plots look
accurate. However, I realized that position restraints were not applied only
after looking at the log files and position restraints energy values were
missing. The umbrella sampling MD simulation was for 2 ns only and I checked
the pullx-umbrella.xvg files and the COM fluctuations are not that bad
considering its only a short time for convergence.
Can anyone comment on how not using position restraints would effect the
result otherwise?
Thanks
--
View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-sampling-position-restraints-tp5010405.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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