[gmx-users] edr file
Justin Lemkul
jalemkul at vt.edu
Fri May 29 19:29:23 CEST 2015
On 5/29/15 1:27 PM, Andrew Bostick wrote:
> Dear gromacs users
>
> After energy minimization, I used g_energy to obtain potential energy vs em
> steps.
>
> g_energy -f em.edr -o potential.xvg.
>
> In potential.xvg, some lines are not seen:
>
> 0.000000 -61742.609375
> 1.000000 -65717.562500
> 2.000000 -75257.804688
> 3.000000 -83263.312500
> 4.000000 -85080.367188
> 5.000000 -86983.921875
> 6.000000 -88253.085938
> 7.000000 -89333.312500
> 8.000000 -90255.179688
> 9.000000 -90895.109375
> 10.000000 -91411.742188
> 11.000000 -91587.226562
> 13.000000 -93838.976562
> 14.000000 -94353.859375
> 15.000000 -97071.710938
> 17.000000 -97458.343750
> 18.000000 -97504.671875
> 19.000000 -97750.882812
> 21.000000 -99023.460938
> 23.000000 -99470.914062
> 24.000000 -99934.640625
> 25.000000 -99989.398438
> 26.000000 -100482.226562
> 28.000000 -100993.773438
> 29.000000 -101070.218750
> 30.000000 -101709.257812
> 32.000000 -102031.210938
> 33.000000 -102141.601562
> 34.000000 -102479.851562
> 36.000000 -102866.414062
> 37.000000 -103024.312500
> 38.000000 -103505.335938
> 40.000000 -103751.210938
> 41.000000 -103878.859375
> 42.000000 -104155.601562
> 44.000000 -104427.421875
> 45.000000 -104673.078125
> 46.000000 -104967.929688
> 47.000000 -105001.984375
> 48.000000 -105314.343750
> 50.000000 -105579.640625
> 51.000000 -105692.773438
> 52.000000 -106005.375000
> 54.000000 -106185.117188
> 55.000000 -106319.828125
> 56.000000 -106503.500000
> 57.000000 -106558.507812
> 58.000000 -106729.734375
> 60.000000 -107011.078125
> 61.000000 -107177.484375
> 62.000000 -107525.437500
> 64.000000 -107655.351562
> 65.000000 -107768.968750
> 66.000000 -107878.164062
> 67.000000 -107959.023438
> 68.000000 -108025.835938
> 69.000000 -108050.921875
> 71.000000 -108464.546875
> 72.000000 -108731.140625
> 73.000000 -109223.937500
> 75.000000 -109300.906250
> 76.000000 -109396.781250
> 77.000000 -109432.421875
> 78.000000 -109495.757812
> 80.000000 -109780.203125
> 81.000000 -109911.140625
> 82.000000 -110282.281250
> 84.000000 -110353.117188
> 85.000000 -110440.046875
> 86.000000 -110473.476562
> 87.000000 -110543.718750
> 89.000000 -110757.671875
> 90.000000 -110862.234375
> 91.000000 -111132.226562
> 93.000000 -111204.718750
> 94.000000 -111269.375000
> 95.000000 -111324.507812
> 96.000000 -111362.320312
> 97.000000 -111384.828125
> 99.000000 -111633.257812
> 100.000000 -111779.343750
> 101.000000 -112095.304688
> 103.000000 -112144.937500
> 104.000000 -112210.242188
> 105.000000 -112230.265625
> 106.000000 -112277.148438
> 108.000000 -112463.078125
> 109.000000 -112530.968750
> 110.000000 -112775.921875
> 112.000000 -112826.421875
> 113.000000 -112881.718750
> 114.000000 -112910.273438
> 115.000000 -112950.132812
> 117.000000 -113104.429688
> 118.000000 -113207.039062
> 119.000000 -113405.992188
> 121.000000 -113454.195312
> 122.000000 -113504.445312
> 123.000000 -113536.109375
> 124.000000 -113572.375000
> 125.000000 -113575.031250
> 126.000000 -113580.210938
> 128.000000 -113816.617188
> 130.000000 -113902.539062
> 131.000000 -113989.375000
> 132.000000 -113993.062500
> 133.000000 -114097.429688
> 135.000000 -114165.523438
> 136.000000 -114189.398438
> 137.000000 -114267.281250
> 139.000000 -114331.078125
> 140.000000 -114371.242188
> 141.000000 -114446.593750
> 143.000000 -114498.906250
> 144.000000 -114543.867188
> 145.000000 -114602.289062
> 146.000000 -114617.218750
> 147.000000 -114679.132812
> 149.000000 -114754.617188
> 150.000000 -114791.828125
> 151.000000 -114885.843750
> 153.000000 -114932.015625
> 154.000000 -114966.289062
> 155.000000 -115013.015625
> 156.000000 -115027.187500
> 157.000000 -115069.609375
> 159.000000 -115161.523438
> 160.000000 -115205.335938
> 161.000000 -115323.750000
> 163.000000 -115362.343750
> 164.000000 -115394.742188
> 165.000000 -115427.054688
> 166.000000 -115446.328125
> 167.000000 -115465.031250
> 169.000000 -115578.031250
> 170.000000 -115656.367188
> 171.000000 -115804.539062
> 173.000000 -115833.648438
> 174.000000 -115869.523438
> 175.000000 -115884.281250
> 176.000000 -115912.750000
> 178.000000 -116000.804688
> 179.000000 -116052.382812
> 180.000000 -116167.679688
> 182.000000 -116198.234375
> 183.000000 -116228.835938
> 184.000000 -116250.265625
> 185.000000 -116272.765625
> 186.000000 -116277.179688
> 187.000000 -116281.867188
> 189.000000 -116421.820312
> 190.000000 -116423.523438
> 191.000000 -116608.437500
> 193.000000 -116625.882812
> 194.000000 -116655.570312
> 196.000000 -116715.117188
> 197.000000 -116770.765625
> 198.000000 -116848.007812
> 200.000000 -116877.164062
> 201.000000 -116904.523438
> 202.000000 -116928.492188
> 203.000000 -116949.664062
> 204.000000 -116963.585938
> 205.000000 -116972.218750
> 207.000000 -117068.375000
> 208.000000 -117126.140625
> 209.000000 -117252.125000
> 211.000000 -117271.906250
> 212.000000 -117299.578125
> 213.000000 -117306.953125
> 214.000000 -117328.593750
> 216.000000 -117401.351562
> 217.000000 -117427.265625
> 218.000000 -117523.335938
> 220.000000 -117545.882812
> 221.000000 -117568.484375
> 222.000000 -117583.343750
> 223.000000 -117599.054688
> 224.000000 -117599.398438
> 225.000000 -117600.062500
> 227.000000 -117718.468750
> 229.000000 -117758.601562
> 230.000000 -117801.531250
> 231.000000 -117801.968750
> 232.000000 -117853.164062
> 234.000000 -117887.453125
> 235.000000 -117898.250000
> 236.000000 -117938.406250
> 238.000000 -117969.632812
> 239.000000 -117988.546875
> 240.000000 -118024.898438
> 242.000000 -118051.781250
> 243.000000 -118075.210938
> 244.000000 -118106.210938
> 245.000000 -118112.515625
> 246.000000 -118146.890625
> 248.000000 -118183.554688
> 249.000000 -118200.015625
> 250.000000 -118244.828125
> 252.000000 -118269.593750
> 253.000000 -118287.210938
> 254.000000 -118313.914062
> 255.000000 -118318.890625
> 256.000000 -118345.671875
> 258.000000 -118389.890625
> 259.000000 -118405.898438
> 260.000000 -118461.867188
> 262.000000 -118483.828125
> 263.000000 -118499.531250
> 264.000000 -118520.640625
> 265.000000 -118526.906250
> 266.000000 -118544.140625
> 268.000000 -118598.179688
> 269.000000 -118619.203125
> 270.000000 -118689.132812
> 272.000000 -118707.437500
> 273.000000 -118723.945312
> 274.000000 -118737.898438
> 275.000000 -118747.695312
> 276.000000 -118753.000000
> 278.000000 -118819.242188
> 279.000000 -118861.054688
> 280.000000 -118947.718750
> 282.000000 -118961.453125
> 283.000000 -118980.648438
> 284.000000 -118985.914062
> 285.000000 -119000.929688
> 287.000000 -119051.132812
> 288.000000 -119070.390625
> 289.000000 -119136.914062
> 291.000000 -119152.718750
> 292.000000 -119168.820312
> 293.000000 -119179.304688
> 294.000000 -119190.859375
> 295.000000 -119191.234375
> 296.000000 -119192.742188
> 298.000000 -119274.101562
> 300.000000 -119302.562500
> 301.000000 -119332.312500
> 302.000000 -119333.710938
> 303.000000 -119369.148438
> 305.000000 -119393.390625
> 306.000000 -119401.976562
> 307.000000 -119430.453125
> 309.000000 -119452.375000
> 310.000000 -119466.625000
> 311.000000 -119492.070312
> 313.000000 -119511.296875
> 314.000000 -119529.000000
> 315.000000 -119551.195312
> 316.000000 -119556.718750
> 317.000000 -119581.437500
> 319.000000 -119607.117188
> 320.000000 -119620.320312
> 321.000000 -119651.601562
> 323.000000 -119669.554688
> 324.000000 -119683.070312
> 325.000000 -119702.531250
> 326.000000 -119707.171875
> 327.000000 -119726.875000
> 329.000000 -119757.804688
> 330.000000 -119771.640625
> 331.000000 -119810.734375
> 333.000000 -119826.968750
> 334.000000 -119839.132812
> 335.000000 -119854.953125
> 336.000000 -119860.523438
> 337.000000 -119873.804688
> 339.000000 -119911.585938
> 340.000000 -119930.562500
> 341.000000 -119979.437500
> 343.000000 -119993.476562
> 344.000000 -120006.203125
> 345.000000 -120017.304688
> 346.000000 -120025.429688
> 347.000000 -120030.601562
> 349.000000 -120076.960938
>
> What is reason of this state?
>
Energy minimization causes energy to go down, hence "minimization."
-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
==================================================
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