[gmx-users] Question regarding calculation of thickness using GridMAT-MD

[Justin Lemkul]

On 3/10/17 10:15 AM, ali.khourshaei71 at student.sharif.edu wrote:
> Dear Gromacs users,
>
> I've used Gridmat-MD to obtain the bilayer thickness and its output is
> as follow:
>
> 4.029
> 4.029
> 4.0735
> 3.928
> 3.9245
> 3.914
> 3.8955
> 4.1755
> 4.349
> 4.349
> 4.426
> 4.236
> 4.236
> 4.1215
> 4.007
> 4.007
> 4.037
> 4.199
> 4.029
> 4.029
> 4.029
> 4.074
> 4.074
> 3.928
> 3.9175
> 3.914
> 3.914
> 4.1315
> 4.349
> 4.349
> 4.2925
> 4.0525
> 4.236
> 4.007
> 3.9445
> 3.9445
> 4.199
> 4.199
> 4.199
> 4.029
> 3.8695
> 4.074
> 4.074
> 3.921
> 3.921
> 3.9365
> 3.933
> 4.1505
> 4.1505
> 3.991
> 3.751
> 3.869
> 3.869
> 3.882
> 3.882
> 4.0405
> 4.199
> 3.997
> 3.73
> 3.8695
> 3.8695
> 4.074
> 4.074
> 3.9975
> 3.921
> 3.9365
> 3.903
> 3.913
> 3.7535
> 3.7535
> 3.751
> 3.869
> 3.869
> 3.8755
> 3.882
> 3.8055
> 3.997
> 3.73
> 3.73
> 3.8695
> 3.9235
> 4.1035
> 3.9445
> 3.9445
> 3.9365
> 3.903
> 3.854
> 3.864
> 3.874
> 3.7535
> 3.716
> 3.834
> 3.834
> 3.61
> 3.8055
> 3.729
> 3.729
> 3.73
> 3.73
> 3.9235
> 4.182
> 4.1035
> 3.9445
> 3.9445
> 3.806
> 3.801
> 3.854
> 3.864
> 3.874
> 3.874
> 3.9225
> 3.885
> 3.7045
> 3.61
> 3.7685
> 3.729
> 3.729
> 3.846
> 3.846
> 4.182
> 4.014
> 4.182
> 3.81
> 3.837
> 3.748
> 3.748
> 3.626
> 3.504
> 3.504
> 4.022
> 4.0705
> 3.885
> 3.6075
> 3.766
> 3.7685
> 4.211
> 4.211
> 3.846
> 3.846
> 4.014
> 3.932
> 3.996
> 3.81
> 3.81
> 3.748
> 3.748
> 3.654
> 3.504
> 3.504
> 4.17
> 4.17
> 3.8875
> 3.6075
> 3.766
> 3.766
> 4.211
> 4.211
> 3.682
> 3.682
> 3.932
> 3.682
> 3.952
> 3.952
> 4.078
> 4.078
> 4.235
> 4.098
> 3.804
> 3.8765
> 4.0595
> 4.0595
> 3.732
> 3.913
> 4.221
> 3.937
> 3.653
> 4.005
> 3.682
> 3.682
> 3.682
> 3.753
> 3.9235
> 4.086
> 4.078
> 4.078
> 4.392
> 4.392
> 3.804
> 3.949
> 3.949
> 3.859
> 3.859
> 4.221
> 4.221
> 3.937
> 3.653
> 3.726
> 3.799
> 3.682
> 3.753
> 3.753
> 3.753
> 4.0895
> 4.252
> 4.1965
> 4.1795
> 4.392
> 4.098
> 4.203
> 3.904
> 3.859
> 3.859
> 4.221
> 4.221
> 3.8845
> 3.6005
> 3.799
> 3.799
> 3.8965
> 3.753
> 3.8965
> 3.753
> 4.155
> 4.2905
> 4.1965
> 4.219
> 4.471
> 4.457
> 4.457
> 4.457
> 3.859
> 3.9615
> 3.83
> 3.7735
> 3.7495
> 3.759
> 3.759
> 3.9195
> 3.8965
> 3.8965
> 3.948
> 3.948
> 4.155
> 4.155
> 4.061
> 4.471
> 4.471
> 4.457
> 4.457
> 4.457
> 4.064
> 4.064
> 3.849
> 3.9
> 3.9
> 3.995
> 3.995
> 4.005
> 4.076
> 3.948
> 4.059
> 4.059
> 4.155
> 4.155
> 3.9815
> 4.471
> 4.398
> 4.351
> 4.377
> 4.377
> 4.064
> 4.064
> 3.849
> 3.849
> 3.9
> 4.02
> 4.02
> 4.112
> 4.112
> 4.059
> 3.939
> 3.939
> 4.266
> 3.9815
> 3.9815
> 4.1395
> 4.296
> 4.351
> 4.377
> 4.377
> 4.064
> 4.015
> 4.1125
> 4.0295
> 4.21
> 4.02
> 4.02
> 4.112
> 4.112
> 3.939
> 3.939
> 3.939
> 4.377
> 4.324
> 4.0395
> 4.267
> 4.267
> 4.267
> 4.3475
> 4.4025
> 4.412
> 4.015
> 4.015
> 4.21
> 4.21
> 4.079
> 3.948
> 3.948
> 3.903
> 3.939
> 3.903
> 4.377
> 4.377
> 4.324
> 4.0395
> 4.269
> 4.267
> 4.267
> 4.3475
> 4.6185
> 4.412
> 4.412
> 4.025
> 4.1225
> 4.0425
> 3.875
> 3.948
> 3.948
> 3.903
> 3.903
> 4.029
> 4.2945
> 4.2945
> 4.2415
> 4.2415
> 3.877
> 4.1755
> 4.474
> 4.474
> 4.809
> 4.809
> 4.035
> 4.035
> 4.035
> 3.875
> 3.875
> 3.7255
> 3.7255
> 3.966
> 4.029
> 4.029
> 4.029
> 4.0735
> 4.0735
> 3.906
> 3.877
> 3.877
> 4.474
> 4.474
> 4.579
> 4.426
> 4.3695
> 4.1355
> 4.021
> 3.941
> 3.875
> 3.7255
> 3.7255
> 4.029
> 4.029
> 4.029
> 4.029
> 4.0735
> 3.928
> 3.9245
> 3.914
> 3.8955
> 4.1755
> 4.349
> 4.349
> 4.426
> 4.236
> 4.236
> 4.1215
> 4.007
> 4.007
> 4.037
> 4.199
> 4.029
> 4.029
>
> So now, should I report the average of the above data as the thickness?
>

You certainly can.  Whether you "should" depends on what you're trying to 
illustrate.

This is not a GROMACS issue, so if you have questions about GridMAT-MD, please 
contact me directly.

-Justin

-- 
==================================================

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

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

==================================================