PBC issues with Radius of Gyration

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juan.salama...@gmail.com

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Oct 12, 2016, 6:41:59 AM10/12/16
to PLUMED users
I'm having troubles calculating the radius of gyration as one CVs. I am using Gromacs 5.1.3 and Plumed 2.3. 

The protein where I'm working is a dimer and on the simulation the Rg change to really high values as10 when the normal value is around 4. See figure below. 




I'm wondering if it its due to PBC issues and that its why I tried to used some WALLS  but didn't work. 

Example of the plumed file ( I'm using the alfa carbons for the Cvs) 

Also I removed some PBC issues with gromacs using -pbc mol -ur compact, -pbc nojump

WHOLEMOLECULES ENTITY0=1-13062

# Rg for C_alfa
GYRATION TYPE=RADIUS ATOMS=5,14,23,37,48,57,66,75,84,93,103,114,122,134,139,147,164,172,185,199,209,226,238,244,254,263,276,289,298,307,316,325,333,339,356,364,373,391,399,409,422,432,440,457,466,483,493,502,511,519,530,535,543,552,558,567,577,590,599,616,630,647,656,665,674,680,685,690,699,708,713,721,730,740,749,763,772,784,793,802,810,818,831,836,845,862,871,880,892,901,910,915,923,928,937,948,961,971,980,989,997,1005,1016,1025,1030,1039,1048,1054,1071,1079,1084,1092,1105,1111,1128,1137,1146,1152,1161,1173,1184,1196,1202,1212,1218,1226,1234,1242,1251,1260,1265,1277,1294,1299,1307,1312,1329,1347,1355,1361,1378,1387,1395,1401,1410,1423,1431,1441,1449,1467,1475,1487,1495,1501,1511,1517,1526,1531,1539,1544,1562,1575,1596,1604,1612,1621,1626,1634,1639,1647,1664,1674,1682,1688,1698,1704,1712,1717,1725,1742,1754,1759,1768,1781,1790,1798,1807,1821,1830,1843,1852,1861,1869,1882,1892,1909,1917,1925,1935,1944,1961,1969,1982,1992,2000,2008,2017,2030,2048,2056,2067,2084,2092,2100,2116,2124,2133,2150,2159,2170,2175,2192,2209,2218,2229,2238,2247,2259,2265,2274,2295,2304,2313,2322,2330,2343,2352,2361,2369,2379,2400,2412,2426,2436,2446,2463,2481,2498,2516,2524,2530,2542,2548,2566,2575,2587,2595,2612,2630,2639,2648,2662,2680,2697,2703,2712,2717,2725,2734,2745,2754,2771,2779,2788,2805,2823,2830,2838,2848,2857,2869,2877,2885,2894,2911,2920,2928,2936,2953,2963,2972,2977,2985,2993,3001,3007,3016,3034,3042,3059,3072,3081,3090,3099,3111,3120,3133,3139,3148,3157,3166,3174,3182,3195,3216,3225,3242,3259,3268,3285,3290,3298,3306,3315,3323,3333,3342,3350,3358,3367,3378,3387,3395,3412,3422,3431,3440,3452,3462,3470,3476,3485,3494,3511,3524,3533,3550,3559,3567,3576,3588,3600,3617,3625,3634,3651,3668,3677,3686,3695,3707,3715,3728,3741,3749,3757,3767,3780,3798,3804,3821,3838,3855,3865,3874,3892,3897,3906,3923,3932,3949,3959,3964,3973,3981,3990,3999,4004,4014,4026,4034,4042,4055,4065,4074,4083,4089,4102,4111,4120,4137,4154,4164,4172,4180,4186,4194,4202,4208,4213,4225,4237,4246,4254,4263,4272,4282,4300,4308,4316,4333,4342,4355,4361,4366,4375,4392,4403,4412,4430,4448,4457,4465,4470,4478,4489,4506,4520,4529,4535,4545,4559,4566,4574,4592,4609,4619,4625,4634,4647,4659,4672,4681,4690,4700,4708,4717,4734,4742,4759,4769,4781,4798,4807,4817,4826,4835,4844,4853,4867,4876,4893,4903,4920,4929,4946,4959,4972,4981,4990,4998,5004,5014,5023,5032,5041,5049,5057,5066,5080,5098,5111,5121,5131,5144,5161,5173,5182,5190,5202,5210,5216,5224,5234,5251,5260,5268,5276,5286,5298,5304,5314,5323,5332,5341,5347,5368,5377,5394,5405,5411,5420,5428,5440,5457,5465,5474,5485,5494,5507,5515,5523,5531,5548,5557,5566,5575,5588,5596,5602,5611,5620,5629,5637,5646,5656,5665,5670,5676,5682,5699,5713,5730,5739,5756,5765,5777,5789,5798,5804,5821,5829,5837,5847,5857,5874,5880,5892,5901,5910,5921,5929,5938,5947,5957,5966,5977,5986,5991,6005,6014,6023,6032,6045,6058,6067,6081,6087,6096,6109,6118,6126,6136,6144,6154,6163,6169,6181,6190,6199,6208,6218,6230,6239,6257,6266,6277,6283,6292,6301,6307,6313,6318,6327,6338,6348,6356,6364,6380,6388,6397,6406,6414,6431,6440,6451,6463,6472,6481,6490,6507,6513,6522,6536,6545,6554,6568,6579,6588,6597,6606,6615,6624,6634,6645,6653,6665,6670,6678,6695,6703,6716,6730,6740,6757,6769,6775,6785,6794,6807,6820,6829,6838,6847,6856,6864,6870,6887,6895,6904,6922,6930,6940,6953,6963,6971,6988,6997,7014,7024,7033,7042,7050,7061,7066,7074,7083,7089,7098,7108,7121,7130,7147,7161,7178,7187,7196,7205,7211,7216,7221,7230,7239,7244,7252,7261,7271,7280,7294,7303,7315,7324,7333,7341,7349,7362,7367,7376,7393,7402,7411,7423,7432,7441,7446,7454,7459,7468,7479,7492,7502,7511,7520,7528,7536,7547,7556,7561,7570,7579,7585,7602,7610,7615,7623,7636,7642,7659,7668,7677,7683,7692,7704,7715,7727,7733,7743,7749,7757,7765,7773,7782,7791,7796,7808,7825,7830,7838,7843,7860,7878,7886,7892,7909,7918,7926,7932,7941,7954,7962,7972,7980,7998,8006,8018,8026,8032,8042,8048,8057,8062,8070,8075,8093,8106,8127,8135,8143,8152,8157,8165,8170,8178,8195,8205,8213,8219,8229,8235,8243,8248,8256,8273,8285,8290,8299,8312,8321,8329,8338,8352,8361,8374,8383,8392,8400,8413,8423,8440,8448,8456,8466,8475,8492,8500,8513,8523,8531,8539,8548,8561,8579,8587,8598,8615,8623,8631,8647,8655,8664,8681,8690,8701,8706,8723,8740,8749,8760,8769,8778,8790,8796,8805,8826,8835,8844,8853,8861,8874,8883,8892,8900,8910,8931,8943,8957,8967,8977,8994,9012,9029,9047,9055,9061,9073,9079,9097,9106,9118,9126,9143,9161,9170,9179,9193,9211,9228,9234,9243,9248,9256,9265,9276,9285,9302,9310,9319,9336,9354,9361,9369,9379,9388,9400,9408,9416,9425,9442,9451,9459,9467,9484,9494,9503,9508,9516,9524,9532,9538,9547,9565,9573,9590,9603,9612,9621,9630,9642,9651,9664,9670,9679,9688,9697,9705,9713,9726,9747,9756,9773,9790,9799,9816,9821,9829,9837,9846,9854,9864,9873,9881,9889,9898,9909,9918,9926,9943,9953,9962,9971,9983,9993,10001,10007,10016,10025,10042,10055,10064,10081,10090,10098,10107,10119,10131,10148,10156,10165,10182,10199,10208,10217,10226,10238,10246,10259,10272,10280,10288,10298,10311,10329,10335,10352,10369,10386,10396,10405,10423,10428,10437,10454,10463,10480,10490,10495,10504,10512,10521,10530,10535,10545,10557,10565,10573,10586,10596,10605,10614,10620,10633,10642,10651,10668,10685,10695,10703,10711,10717,10725,10733,10739,10744,10756,10768,10777,10785,10794,10803,10813,10831,10839,10847,10864,10873,10886,10892,10897,10906,10923,10934,10943,10961,10979,10988,10996,11001,11009,11020,11037,11051,11060,11066,11076,11090,11097,11105,11123,11140,11150,11156,11165,11178,11190,11203,11212,11221,11231,11239,11248,11265,11273,11290,11300,11312,11329,11338,11348,11357,11366,11375,11384,11398,11407,11424,11434,11451,11460,11477,11490,11503,11512,11521,11529,11535,11545,11554,11563,11572,11580,11588,11597,11611,11629,11642,11652,11662,11675,11692,11704,11713,11721,11733,11741,11747,11755,11765,11782,11791,11799,11807,11817,11829,11835,11845,11854,11863,11872,11878,11899,11908,11925,11936,11942,11951,11959,11971,11988,11996,12005,12016,12025,12038,12046,12054,12062,12079,12088,12097,12106,12119,12127,12133,12142,12151,12160,12168,12177,12187,12196,12201,12207,12213,12230,12244,12261,12270,12287,12296,12308,12320,12329,12335,12352,12360,12368,12378,12388,12405,12411,12423,12432,12441,12452,12460,12469,12478,12488,12497,12508,12517,12522,12536,12545,12554,12563,12576,12589,12598,12612,12618,12627,12640,12649,12657,12667,12675,12685,12694,12700,12712,12721,12730,12739,12749,12761,12770,12788,12797,12808,12814,12823,12832,12838,12844,12849,12858,12869,12879,12887,12895,12911,12919,12928,12937,12945,12962,12971,12982,12994,13003,13012,13021,13038,13044,13053 LABEL=rg

UPPER_WALLS ARG=rg AT=6 KAPPA=1000.0

# Calculate the center of mass for a group of atoms (with label at the begining)
NtA: COM ATOMS=164,172,185,199,209,226,238,244,254,263,276,289,298,307,316,325,333,339,356,364,373,391,399,409,422,432,440,457,466,483,493,502,511,519,530,535,543,552,558,567,577,590,599,616,630,647,656,665,674,680,685,690,699,708,713,721,730,740,749,763,772,784,793,802,810,818,831,836,845,862,871,880,892,901,910,915,923,928,937,948,961,971,980,989,997,1005,1016,1025,1030,1039,1048,1054,1071,1079,1084,1092,1105,1111,1128,1137,1146,1152,1161,1173,1184,1196,1202,1212,1218,1226,1234,1242,1251,1260,1265,1277,1294,1299,1307,1312,1329,1347,1355,1361,1378,1387,1395,1401,1410,1423,1431,1441,1449,1467,1475,1487,1495,1501,1511,1517,1526,1531,1539,1544,1562,1575,1596,1604,1612,1621,1626,1634,1639,1647,1664,1674,1682,1688,1698,1704,1712,1717,1725,1742,1754,1759,1768,1781,1790,1798,1807,1821,1830,1843,1852,1861,1869,1882,1892,1909,1917,1925,1935,1944,1961,1969,1982,1992,2000,2008,2017,2030,2048,2056,2067,2084,2092,2100,2116,2124,2133,2150,2159,2170,2175,2192,2209,2218 

NtB: COM ATOMS=6695,6703,6716,6730,6740,6757,6769,6775,6785,6794,6807,6820,6829,6838,6847,6856,6864,6870,6887,6895,6904,6922,6930,6940,6953,6963,6971,6988,6997,7014,7024,7033,7042,7050,7061,7066,7074,7083,7089,7098,7108,7121,7130,7147,7161,7178,7187,7196,7205,7211,7216,7221,7230,7239,7244,7252,7261,7271,7280,7294,7303,7315,7324,7333,7341,7349,7362,7367,7376,7393,7402,7411,7423,7432,7441,7446,7454,7459,7468,7479,7492,7502,7511,7520,7528,7536,7547,7556,7561,7570,7579,7585,7602,7610,7615,7623,7636,7642,7659,7668,7677,7683,7692,7704,7715,7727,7733,7743,7749,7757,7765,7773,7782,7791,7796,7808,7825,7830,7838,7843,7860,7878,7886,7892,7909,7918,7926,7932,7941,7954,7962,7972,7980,7998,8006,8018,8026,8032,8042,8048,8057,8062,8070,8075,8093,8106,8127,8135,8143,8152,8157,8165,8170,8178,8195,8205,8213,8219,8229,8235,8243,8248,8256,8273,8285,8290,8299,8312,8321,8329,8338,8352,8361,8374,8383,8392,8400,8413,8423,8440,8448,8456,8466,8475,8492,8500,8513,8523,8531,8539,8548,8561,8579,8587,8598,8615,8623,8631,8647,8655,8664,8681,8690,8701,8706,8723,8740,8749 

Ct: COM ATOMS=5224,5234,5251,5260,5268,5276,5286,5298,5304,5314,5323,5332,5341,5347,5368,5377,5394,5405,5411,5420,5428,5440,5457,5465,5474,5485,5494,5507,5515,5523,5531,5548,5557,5566,5575,5588,5596,5602,5611,5620,5629,5637,5646,5656,5665,5670,5676,5682,5699,5713,5730,5739,5756,5765,5777,5789,5798,5804,5821,5829,5837,5847,5857,5874,5880,5892,5901,5910,5921,5929,5938,5947,5957,5966,5977,5986,5991,6005,6014,6023,6032,6045,6058,6067,6081,6087,6096,6109,6118,6126,6136,6144,6154,6163,6169,6181,6190,6199,6208,6218,6230,6239,6257,6266,6277,6283,6292,6301,6307,6313,6318,6327,6338,6348,6356,6364,6380,6388,6397,6406,6414,6431,6440,6451,6463,6472,6481,6490,6507,6513,6522,11755,11765,11782,11791,11799,11807,11817,11829,11835,11845,11854,11863,11872,11878,11899,11908,11925,11936,11942,11951,11959,11971,11988,11996,12005,12016,12025,12038,12046,12054,12062,12079,12088,12097,12106,12119,12127,12133,12142,12151,12160,12168,12177,12187,12196,12201,12207,12213,12230,12244,12261,12270,12287,12296,12308,12320,12329,12335,12352,12360,12368,12378,12388,12405,12411,12423,12432,12441,12452,12460,12469,12478,12488,12497,12508,12517,12522,12536,12545,12554,12563,12576,12589,12598,12612,12618,12627,12640,12649,12657,12667,12675,12685,12694,12700,12712,12721,12730,12739,12749,12761,12770,12788,12797,12808,12814,12823,12832,12838,12844,12849,12858,12869,12879,12887,12895,12911,12919,12928,12937,12945,12962,12971,12982,12994,13003,13012,13021,13038,13044,13053

a: ANGLE ATOMS=NtA,NtB,Ct 
UPPER_WALLS ARG=a AT=1.6 KAPPA=1000.0
# 3rd CV ?NOPBC
dist: DISTANCE ATOMS=NtA,NtB 
UPPER_WALLS ARG=dist AT=10 KAPPA=1000.0

#For each CVs, one has to specified the width of the Gaussian by using the keyword SIGMA. Gaussian will be written to the file indicated by the keyword FILE.

wte: METAD ARG=rg,a,dist PACE=500 HEIGHT=0.5 SIGMA=0.35,0.35,0.35 FILE=HILLS BIASFACTOR=8 TEMP=300

# Print all the values in the colvar_ptwte
PRINT ARG=rg,a,dist,wte.bias STRIDE=500 FILE=COLVAR

I hope you could help me, thank you so much for your time, 

Juan S

Carlo Camilloni

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Oct 12, 2016, 7:27:57 AM10/12/16
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If the protein is a dimer using WHOLEMOLECULES ENTITY0=1-13062 could not be optimal
because it will try to put consecutive atoms in the same periodic cell but for example the last
atom of the first monomer and the first atom of the second could be very far apart. So you
should order the atoms in a way that atoms are likely close in space, for example if your
dimers have two atoms (100 and 11000 for example) that are always close you can do something like


ENTITY0=1-100,11000-13062,13062-FirstOfSecondMonomer:-1,FirstOfSecondMonomer-11000,100-LastOfFirstMonomer

Anyway the radius of gyration makes sense only if the two are always bound and you can define something like the above..

In addition you should calculate GYRATION … NOPBC because otherwise GYRATION will automatically try to make the
atoms ‘whole’.

Carlo


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Giovanni Bussi

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Oct 12, 2016, 8:03:07 AM10/12/16
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Hi!

An extra hint: your simulation might become very slow using that many atoms. This could be alleviated using less atoms, and/or using multiple time stepping (http://plumed.github.io/doc-v2.3/user-doc/html/_m_t_s.html).

Giovanni


On Wed, Oct 12, 2016 at 1:27 PM, Carlo Camilloni <carlo.c...@gmail.com> wrote:
If the protein is a dimer using WHOLEMOLECULES ENTITY0=1-13062 could not be optimal
because it will try to put consecutive atoms in the same periodic cell but for example the last
atom of the first monomer and the first atom of the second could be very far apart. So you
should order the atoms in a way that atoms are likely close in space, for example if your
dimers have two atoms (100 and 11000 for example) that are always close you can do something like


ENTITY0=1-100,11000-13062,13062-FirstOfSecondMonomer:-1,FirstOfSecondMonomer-11000,100-LastOfFirstMonomer

Anyway the radius of gyration makes sense only if the two are always bound and you can define something like the above..

In addition you should calculate GYRATION … NOPBC because otherwise GYRATION will automatically try to make the
atoms ‘whole’.

Carlo
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