[gmx-users] How to define pull-init for two pull groups
Rini Gupta
rinisgupta at gmail.com
Sat Jan 18 02:06:14 CET 2014
Dear gmx-users,
Thanks for the reply.
That means if I will use the frames generated by script (setup-umbrella.py)
it will not generate a sufficient overlap between adjacent
windows for this system?
So, In order to extract starting window structures for umbrella sampling of
my system I prepared a list of frames at a distance of 0.1 nm
including frames where distance between reference group and pull group is
decreasing in steps of 0.1 nm and then increasing by same amount.
Please let me know if this is right.
Then, in order to equilibrate each of these initial configuration, I use
the following .mdp settings (as given by tutorial)
> ; Pull code
> pull = umbrella
> pull_geometry = position ;
> pull_dim = N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 2
> pull_group0 = cbilayer ; center of carbon's of bilayer
> pull_group1 = phosup ; phosphate atom of 16th PEPC in top
> pull_pbcatom1 = 0
> pull_vec1 = 0.0 0.0 -1.0
> pull_init1 = 0 0 0
> pull_rate1 = 0 ; no pulling
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
> pull_group2 = phoslow ; phosphate atom of 56th PEPC in bottom
> pull_pbcatom2 = 0
> pull_vec2 = 0.0 0.0 1.0
> pull_init2 = 0 0 0
> pull_rate2 = 0 ; no pulling
> pull_k2 = 1000 ; kJ mol^-1 nm^-2
> pull_nstxout = 100 ; every 2 ps
> pull_nstfout = 100 ; every 2 ps
>
>
After equilibration of 4 ns, if I want to extend these runs for longer
time using tpbconv:
# tpbconv_mpi_d -f npt0.trr -s npt0.tpr -e npt0.edr -n index.ndx -extend
2000 -o npt0.tpr
# mdrun_mpi_d -s npt0.tpr -cpi npt0.cpt -deffnm ${MDRUN_RUN_NAME}
----------------------------------------------------------------------------------------------------------------------
Program tpbconv_mpi_d, VERSION 4.6.2
Source code file: /home/roman/gromacs-4.6.2/src/gmxlib/index.c, line: 1192
Fatal error:
Cannot read from input
and
Program mdrun_mpi_d, VERSION 4.6.2
Source code file: /home/roman/gromacs-4.6.2/src/gmxlib/checkpoint.c, line:
2118
Fatal error:
Can't read 34580 bytes of 'npt0.xvg' to compute checksum. The file has been
replaced or its contents have been modified. Cannot do appending because of
this condition.
----------------------------------------------------------------------------------------------------------------------------------------------------
Please let me what is wrong here, I did not modify any file after 4 ns and
I have been successfully extending normal simulation runs (without pull
code) using these settings.
So, I guess here problem is related to
generation of *.xvg file.
How to supply this file to tpbconv? I have searched on mailing list but
didn’t get any satisfactory answer for extending equilibration or even
production runs (which generate pullf.xvg and pullx.xvg files)
for these umbrella sampling simulations.
Thanks and Regards,
Rini
On 1/14/14, 8:23 PM, Rini Gupta wrote:
> Dear gmx-users,
>
> Thanks for the nice reply.
>
> I have corrected the pull code as:
>
>
>
> ; Pull code
> pull = umbrella
> pull_geometry = position ;
> pull_dim = N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 2
> pull_group0 = cbilayer ; center of carbon's of bilayer
> pull_group1 = phosup ; phosphate atom of 16th PEPC in top
> pull_pbcatom1 = 0
> pull_vec1 = 0.0 0.0 -1.0
> pull_init1 = 0 0 0
> pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
> pull_group2 = phoslow ; phosphate atom of 56th PEPC in bottom
> pull_pbcatom2 = 0
> pull_vec2 = 0.0 0.0 1.0
> pull_init2 = 0 0 0
> pull_rate2 = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_k2 = 1000 ; kJ mol^-1 nm^-2
>
> Now, after extracting trajectory frames and measuring the distances between
> COM distances between two pull groups and a reference group, I found that
> values of summary_distances.dat are first decreasing through roughly half
> of the frames and then start increasing till final frame.
> The snapshots are also matching the output.
> If this is right for a lipid crossing through bilayer then in order to
> generate starting configurations at windows spacing of 0.06 nm I ran the
> script (setup-umbrella.py) link provided in tutorial.
> But, the output file (caught_output.txt) which contain the list of initial
> frames with distances
> select only frames after half of the times frames.
> i.e If I provide a .dat file corresponding to 400 time frames it produces
> the list of frames at a desired spacing excluding the frames where distance
> between reference and pull group is decreasing . I got :
>
> Creating frame-specific output for files:
> run-umbrella.sh
> frame dist d_dist
> 0 3.082 NA
> 6 3.137 0.055
> 222 3.215 0.078
> 224 3.272 0.057
> 228 3.320 0.049
> 230 3.380 0.060
> 231 3.427 0.047
> 237 3.495 0.068
> 239 3.557 0.062
> 240 3.619 0.062
> 242 3.720 0.102
> 257 3.781 0.061
> 271 3.835 0.053
> 272 3.894 0.059
> 283 3.935 0.041
> 286 4.010 0.075
> 288 4.063 0.053
> 299 4.113 0.049
> 300 4.188 0.075
> 302 4.243 0.055
> 305 4.303 0.060
> 311 4.397 0.094
> 312 4.431 0.034
>
>
> If this is case, how it will generate a sufficient overlap between adjacent
> windows ?
>
> Also, script works only for single lipid pulling out of a layer. It is
> possible to use it for two lipids simultaneously crossing the bilayer in
> different directions.
>
>
Don't try to apply the scripts in the tutorial too literally. You're doing
something much more complex than what the tutorial did and what those
scripts are designed for. You can apply the same logic, but will probably
have to come up with your own scripts to extract pertinent information.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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