Hi Dr. Roitberg,
I have pulled the group of atoms using the following code:
ASMD Simulation Example MD Input
&cntrl
imin = 0, nstlim = 300000, dt = 0.001,
ntx = 1, temp0 = 300.0,
ntt = 3, gamma_ln=5.0
ntc = 2, ntf = 2, ntb =1,
ntwx = 1000, ntwr = 1000, ntpr = 1000,
cut = 10.0, ig=-1, ioutfm=1,
irest = 0, jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=shear200.RST
DUMPAVE=distshear200_vs_t
LISTIN=POUT
LISTOUT=POUT
&rst
iat=-1,-1,
r2=0.0,
rk2=200,
r2a=350.0,
iresid=0,
fxyz=0,0,1,
outxyz=1,
igr1=3,24,45,66,87,108,129,150,171,192,213,234,255,276,297,318,342,363,384,405,426,447,468,489,510,531,552,573,594,615,636,657,681,702,723,744,765,786,807,828,849,870,891,912,933,954,975,996,1020,1041,1062,1083,1104,1125,1146,1167,1188,1209,1230,1251,1272,1293,1314,1335,1359,1380,1401,1422,1443,1464,1485,1506,1527,1548,1569,1590,1611,1632,1653,1674,1698,1719,1740,1761,1782,1803,1824,1845,1866,1887,1908,1929,1950,1971,1992,2013,2037,2058,2079,2100,2121,2142,2163,2184,2205,2226,2247,2268,2289,2310,2331,2352,2376,2397,2418,2439,2460,2481,2502,2523,2544,2565,2586,2607,2628,2649,2670,2691,2715,2736,2757,2778,2799,2820,2841,2862,2883,2904,2925,2946,2967,2988,3009,3030,3054,3075,3096,3117,3138,3159,3180,3201,3222,3243,3264,3285,3306,3327,3348,3369,3393,3414,3435,3456,3477,3498,3519,3540,3561,3582,3603,3624,3645,3666,3687,3708,3732,3753,3774,3795,3816,3837,3858,3879,3900,3921,3942,3963,3984,4005,4026,4047,4071,4092,4113,4134,4155,4176,4197,4218,4239,4260,4281,4302,4323,4344,4365,4386,4410,4431,4452,4473,4494,4515,45
36,4557,4578,4599,4620,4641,4662,4683,4704,4725,4749,4770,4791,4812,4833,4854,4875,4896,4917,4938,4959,4980,5001,5022,5043,5064,5088,5109,5130,5151,5172,5193,5214,5235,5256,5277,5298,5319,5340,5361,5382,5403,5427,5448,5469,5490,5511,5532,5553,5574,5595,5616,5637,5658,5679,5700,5721,5742,5766,5787,5808,5829,5850,5871,5892,5913,5934,5955,5976,5997,6018,6039,6060,6081,6105,6126,6147,6168,6189,6210,6231,6252,6273,6294,6315,6336,6357,6378,6399,6420,6444,6465,6486,6507,6528,6549,6570,6591,6612,6633,6654,6675,6696,6717,6738,6759,6783,6804,6825,6846,6867,6888,6909,6930,6951,6972,6993,7014,7035,7056,7077,7098,7122,7143,7164,7185,7206,7227,7248,7269,7290,7311,7332,7353,7374,7395,7416,7437,7461,7482,7503,7524,7545,7566,7587,7608,7629,7650,7671,7692,7713,7734,7755,7776,7800,7821,7842,7863,7884,7905,7926,7947,7968,7989,8010,8031,8052,8073,8094,8115,8139,8160,8181,8202,8223,8244,8265,8286,8307,8328,8349,8370,8391,8412,8433,8454,8478,8499,8520,8541,8562,8583,8604,8625,8646,8667,8688,8709,8730,8751,8772,8793,8817,8838,8859,
8880,8901,8922,8943,8964,8985,9006,9027,9048,9069,9090,9111,9132,9156,9177,9198,9219,9240,9261,9282,9303,9324,9345,9366,9387,9408,9429,9450,9471,9495,9516,9537,9558,9579,9600,9621,9642,9663,9684,9705,9726,9747,9768,9789,9810,9834,9855,9876,9897,9918,9939,9960,9981,10002,10023,10044,10065,10086,10107,10128,10149,
igr2=18527,18548,18569,18590,18611,18632,18653,18674,18695,18716,18737,18758,18779,18800,18821,18842,18866,18887,18908,18929,18950,18971,18992,19013,19034,19055,19076,19097,19118,19139,19160,19181,19205,19226,19247,19268,19289,19310,19331,19352,19373,19394,19415,19436,19457,19478,19499,19520,19544,19565,19586,19607,19628,19649,19670,19691,19712,19733,19754,19775,19796,19817,19838,19859,19883,19904,19925,19946,19967,19988,20009,20030,20051,20072,20093,20114,20135,20156,20177,20198,20222,20243,20264,20285,20306,20327,20348,20369,20390,20411,20432,20453,20474,20495,20516,20537,20561,20582,20603,20624,20645,20666,20687,20708,20729,20750,20771,20792,20813,20834,20855,20876,20900,20921,20942,20963,20984,21005,21026,21047,21068,21089,21110,21131,21152,21173,21194,21215,21239,21260,21281,21302,21323,21344,21365,21386,21407,21428,21449,21470,21491,21512,21533,21554,21578,21599,21620,21641,21662,21683,21704,21725,21746,21767,21788,21809,21830,21851,21872,21893,21917,21938,21959,21980,22001,22022,22043,22064,22085,2210
6,22127,22148,22169,22190,22211,22232,22256,22277,22298,22319,22340,22361,22382,22403,22424,22445,22466,22487,22508,22529,22550,22571,22595,22616,22637,22658,22679,22700,22721,22742,22763,22784,22805,22826,22847,22868,22889,22910,22934,22955,22976,22997,23018,23039,23060,23081,23102,23123,23144,23165,23186,23207,23228,23249,23273,23294,23315,23336,23357,23378,23399,23420,23441,23462,23483,23504,23525,23546,23567,23588,23612,23633,23654,23675,23696,23717,23738,23759,23780,23801,23822,23843,23864,23885,23906,23927,23951,23972,23993,24014,24035,24056,24077,24098,24119,24140,24161,24182,24203,24224,24245,24266,24290,24311,24332,24353,24374,24395,24416,24437,24458,24479,24500,24521,24542,24563,24584,24605,24629,24650,24671,24692,24713,24734,24755,24776,24797,24818,24839,24860,24881,24902,24923,24944,24968,24989,25010,25031,25052,25073,25094,25115,25136,25157,25178,25199,25220,25241,25262,25283,25307,25328,25349,25370,25391,25412,25433,25454,25475,25496,25517,25538,25559,25580,25601,25622,25646,25667,25688,25709,2
5730,25751,25772,25793,25814,25835,25856,25877,25898,25919,25940,25961,25985,26006,26027,26048,26069,26090,26111,26132,26153,26174,26195,26216,26237,26258,26279,26300,26324,26345,26366,26387,26408,26429,26450,26471,26492,26513,26534,26555,26576,26597,26618,26639,26663,26684,26705,26726,26747,26768,26789,26810,26831,26852,26873,26894,26915,26936,26957,26978,27002,27023,27044,27065,27086,27107,27128,27149,27170,27191,27212,27233,27254,27275,27296,27317,27341,27362,27383,27404,27425,27446,27467,27488,27509,27530,27551,27572,27593,27614,27635,27656,27680,27701,27722,27743,27764,27785,27806,27827,27848,27869,27890,27911,27932,27953,27974,27995,28019,28040,28061,28082,28103,28124,28145,28166,28187,28208,28229,28250,28271,28292,28313,28334,28358,28379,28400,28421,28442,28463,28484,28505,28526,28547,28568,28589,28610,28631,28652,28673,
/
Now, the simulation looks fine but didn't get the desired
force-displacement curve.
I do not know where I am doing wrong?
On Fri, Feb 26, 2021 at 10:14 AM Adrian Roitberg <roitberg.ufl.edu> wrote:
> not really... You need to pull the CENTER of mass of lots of atoms,
> which is not the same, right ?
>
> I believe the error you got in your second attempt was related to the
> maximum number of atoms you can have in a given group.
>
> Look at page 27 of the AMBER 20 manual.
>
> You can have MAXIMUM 200 atoms in a group, and it is possible you have
> more.
>
>
> So, there are two options:
>
>
> 1. Change the value of I think the variable MAXGRP in the actual code,
> and recompile. If you never changed the code/recompiled, I would not
> recommend this.
>
> 2. Reduce the number of atoms in your group mask. I am betting you can
> look at the atoms you choose and reduced it by half. For example, if you
> list all CA atoms in your molecule, list instead every OTHER CA atom.
>
>
> More general comments.
>
>
> Your input (and I do think you want to use jar, NOT nmropt)
>
> which is WAY too fast
>
>
> &rst
>
> iat=2709,1365,
>
> r2=72.67,
>
> r2a=0.0,
>
> rk2=7.2,
>
> &end
>
>
> Your input (and I do think you want to use jar, NOT nmropt)
>
> is trying to go from 72 A to zero A in 20K steps, which is WAY to fast.
>
>
> Moreover, you truly do not wan to go to zero ! You want to go to the
> minimal distance possible between your two groups of atoms.
>
>
> Adrian
>
>
> On 2/26/21 10:43 AM, Pinky Mazumder wrote:
> > [External Email]
> >
> > Hi Dr. Roitberg,
> >
> > It is fine when I selected only two atoms. But I need to pull many atoms
> > together.
> >
> > Thank you!
> >
> > Sincerely,
> > Pinky
> >
> > On Thu, Feb 25, 2021 at 2:22 PM Adrian Roitberg <roitberg.ufl.edu>
> wrote:
> >
> >> Hi
> >>
> >> Try first with just a couple of atoms in your ref.RST file like:
> >>
> >> &rst
> >> iat=2709,1365,
> >> r2=72.67,
> >> r2a=0.0,
> >> rk2=7.2,
> >> &end
> >>
> >> to see if it works.
> >>
> >> Second, are you sure you want to have r2a = 0.0 ? that will try to have
> >> the two gropus of atoms get to ZERO distance, which I believe will (and
> >> should) break everything).
> >>
> >> Adrian
> >>
> >>
> >> On 2/25/21 3:14 PM, Pinky Mazumder wrote:
> >>> [External Email]
> >>>
> >>> Hi,
> >>>
> >>> I am trying to pull one layer (group of atoms) towards another group of
> >>> atoms using the steered molecular dynamics. I have taken the center of
> >> mass
> >>> of both groups. The (.RST) and (pull.in) file is given below:
> >>>
> >>> &rst
> >>> iat=-1,-1,
> >>> r2=72.67,
> >>> r2a=0.0,
> >>> rk2=7.2,
> >>>
> >>>
> >>
> igr1=2709,2730,2751,2772,2793,2814,2835,2856,2877,2898,2919,2940,2961,2982,3003,3024,3048,3069,3090,3111,3132,3153,3174,3195,3216,3237,3258,3279,3300,3321,3342,3363,3386,3407,3428,3449,3470,3491,3512,3533,3554,3575,3596,3617,3638,3659,3680,3701,3725,3746,3767,3788,3809,3830,3851,3872,3893,3914,3935,3956,3977,3998,4019,4040,
> >>>
> >>
> igr2=1365,1386,1407,1428,1449,1470,1491,1512,1533,1554,1575,1596,1617,1638,1659,1680,1704,1725,1746,1767,1788,1809,1830,1851,1872,1893,1914,1935,1956,1977,1998,2019,2042,2063,2084,2105,2126,2147,2168,2189,2210,2231,2252,2273,2294,2315,2336,2357,2381,2402,2423,2444,2465,2486,2507,2528,2549,2570,2591,2612,2633,2654,2675,2696,
> >>> &end
> >>>
> >>> ASMD Simulation Example MD Input
> >>> &cntrl
> >>> imin = 0, nstlim = 20000, dt = 0.002,
> >>> ntx = 1, temp0 = 300.0,
> >>> ntt = 3, gamma_ln=5.0
> >>> ntc = 2, ntf = 2, ntb =1,
> >>> ntwx = 1000, ntwr = 1000, ntpr = 1000,
> >>> cut = 10.0, ig=-1, ioutfm=1,
> >>> irest = 0, jar=1,
> >>> /
> >>> &wt type='DUMPFREQ', istep1=1, /
> >>> &wt type='END', /
> >>> DISANG=ref.RST
> >>> DUMPAVE=ref_vs_t
> >>> LISTIN=POUT
> >>> LISTOUT=POUT
> >>>
> >>> When I am running simulation, it gives following error:
> >>> Restraints will be read from file: ref.RST
> >>> Here are comments from the DISANG input file:
> >>>
> >>>
> >>> *jar option running In Jarzynsky runs, there must only one restrain,
> >>> stopping program*
> >>>
> >>> Any help would be appreciated.
> >>>
> >>> Thank you.
> >>>
> >>> Sincerely,
> >>> Pinky
> >>> --
> >>> Pinky Mazumder
> >>> PhD Student
> >>> University of Alabama
> >>> USA
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>>
> >>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=CqzFAWPdYovbmAUpZxFIQmJyYQsg1VPbDKFo44ZS3Mk&s=E1NdBtoYo7MxU2SXucvPmNBQvS1_Fm682XT-ZCq6FrQ&e=
> >>
> >> --
> >> Dr. Adrian E. Roitberg
> >> V.T. and Louise Jackson Professor in Chemistry
> >> Department of Chemistry
> >> University of Florida
> >> roitberg.ufl.edu
> >> 352-392-6972
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=g2rPo9g3dRq2TKBjbS-t7nLEDfeLo3QTb0jh7o5gt9w&s=QoaWPYejd0MOBUO4s85XaUR9hrLrqoPUAdG0eb20LKM&e=
> >>
> >
> > --
> > Pinky Mazumder
> > PhD Student
> > University of Alabama
> > USA
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=g2rPo9g3dRq2TKBjbS-t7nLEDfeLo3QTb0jh7o5gt9w&s=QoaWPYejd0MOBUO4s85XaUR9hrLrqoPUAdG0eb20LKM&e=
>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pinky Mazumder
PhD Student
University of Alabama
USA
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Received on Sat Feb 27 2021 - 07:00:02 PST
