[gmx-users] Umbrella Sampling on Lipid Bilayers, Pulling Issue and Umbrella Sampling Window Simulation Issues.
Justin Lemkul
jalemkul at vt.edu
Mon Nov 4 20:43:04 CET 2019
On 11/1/19 2:09 PM, Alexander Phillips wrote:
> Hello Everyone,
>
> I am currently running a CG MARTINI simulation on a bilayer of POPC Lipid
> in Water. I also have a single vitamin E in the mixture aswell (inside of
> the POPC bilayer). I am trying to perform umbrella sampling by pulling the
> vitamin E and measuring it's binding energy to POPC. I am basing most of my
> work off of the tutorial made by Justin Lemkul. The plan for my umbrella
> sampling is to pull the vitamin E vertically out of the membrane (from the
> center of the membrane to some distance into the water). However I am
> having issues with performing umbrella sampling. I believe the issue is one
> of two things (or perhaps a mixture of both):
> 1) The simulation where I pull the Vitamin E out of POPC is happenning too
> quickly and I cannot gather enough frames to get valid input windows for
> the umbrella sampling portion.
> 2) The umbrella sampling portion is not keeping the Vitamin E around the
> starting portion and it falls back into the membrane.
>
> I will attach the mdp files I used for both, and hopefully someone can give
> me some advice about how to do this / fix it.
It may be a combination of things. Your pull rate is quite fast and your
force constant is very small. I suggest experimenting with slower
pulling and/or a stiffer spring constant.
> I am running in Gromacs 4.6.5 so a few things are changed from the files
> given in Justin's tutorial, however I believe ultimately it's about the
> same.
Any reason to use such antiquated software? The modern versions will be
MUCH faster (and are actually supported by the developers in case of
problems).
-Justin
> Here is the mdp for the Pulling:
>
>
> integrator = md
> dt = 0.03
> nsteps = 250000
> nstcomm = 10
>
> comm-grps =
> nstxout = 5000
> nstvout = 5000
> nstfout = 5000
> nstlog = 1000 ; Output frequency for energies to log file
> nstenergy = 100 ; Output frequency for energies to energy file
> nstxtcout = 1000 ; Output frequency for .xtc file
> xtc_precision = 5
> xtc-grps =
>
> energygrps = Lipids Solvent PULLING_ATOC
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 1.4
> coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME
> (especially with polarizable water)
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> epsilon_r = 15 ; 2.5 (with polarizable water)
> vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
> rvdw_switch = 0.9
> rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
>
> tcoupl = v-rescale
> tc-grps = Lipids Solvent PULLING_ATOC
> tau_t = 1.0 1.0 1.0
> ref_t = 310 310 310
> Pcoupl = parrinello-rahman
> Pcoupltype = semiisotropic
> tau_p = 12.0 12.0 12.0 ;parrinello-rahman is more stable
> with larger tau-p, DdJ, 20130422
> compressibility = 3e-4 3e-4 3e-4
> ref_p = 1.0 1.0 1.0
>
> gen_vel = no
> gen_temp = 310
> gen_seed = 473529
>
> constraints = none
> constraint_algorithm = Lincs
> continuation = no
> lincs_order = 4
> lincs_warnangle = 30
>
> ; Pull Code
> pull = umbrella
> pull-geometry = direction-periodic
> pull-start = yes
> pull-nstxout = 10
> pull-nstfout = 10
> pull-ngroups = 1
> pull-group0 = Lipids
> pull-group1 = PULLING_ATOC
> pull-vec1 = 0 0 1
> pull-rate1 = 0.01
> pull-k1 = 20
>
>
>
>
> ---------------------------------------------------------------- End of MDP
> 1 -----------------------
>
> The second MDP file (the one used for the Umbrella Sampling production run)
> is listed here
>
> integrator = md
> dt = 0.002
> nsteps = 10000000
> nstcomm = 10
> comm-grps =
>
> nstxout = 50000
> nstvout = 50000
> nstfout = 5000
> nstlog = 1000 ; Output frequency for energies to log
> file
> nstenergy = 5000 ; Output frequency for energies to energy
> file
> nstxtcout = 5000 ; Output frequency for .xtc file
> xtc_precision = 100
> xtc-grps =
> energygrps = Lipids Solvent PULLING_ATOC
>
> nstlist = 5
> ns_type = grid
> pbc = xyz
> rlist = 1.4
>
> coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist)
> ;PME (especially with polarizable water)
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> epsilon_r = 15 ; 2.5 (with polarizable water)
> vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
> rvdw_switch = 0.9
> rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
>
> tcoupl = v-rescale
> tc-grps = Lipids Solvent PULLING_ATOC
> tau_t = 1.0 1.0 1.0
> ref_t = 310 310 310
> Pcoupl = parrinello-rahman
> Pcoupltype = semiisotropic
> tau_p = 12.0 12.0 12.0 ;parrinello-rahman is more
> stable with larger tau-p, DdJ, 20130422
> compressibility = 3e-4 3e-4 3e-4
> ref_p = 1.0 1.0 1.0
>
> gen_vel = no
> gen_temp = 310
> gen_seed = 473529
>
> constraints = none
> constraint_algorithm = Lincs
> continuation = no
> lincs_order = 4
> lincs_warnangle = 30
>
> ; Pull Code
> pull = umbrella
> pull-geometry = direction-periodic
> pull-start = yes
> pull-nstxout = 10
> pull-nstfout = 10
> pull-ngroups = 1
> pull-group0 = Lipids
> pull-group1 = PULLING_ATOC
> pull-vec1 = 0 0 1
> pull-rate1 = 0
> pull-k1 = 1
>
> ---------------------------- END of MDP 2 -------------------
>
>
> If you have any questions, please ask and I will try my best to answer
> them, Thank you,
> Alex
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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