Thanks for the advice
I have performed before a simple MD with the system so I think that the TI will be easy, but the TI doesn't work. So I this point, and because I'm new, I don't know how I can solve this problem
But thanks for all of the help
Best regards
Vero
________________________________
De: Steinbrecher, Thomas <thomas.steinbrecher.roche.com>
Enviado: martes, 19 de marzo de 2024 8:21
Para: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es>
Asunto: Re: [Sender Not Verified] Re: [AMBER] AMBER error vlimit exceed for step
Hi Vero,
the first advice is always, does a plain MD of this system work as expected, before you do any debugging of free energy runs.
second, nothing obviously wrong with your input file, apart from using ntc/ntf=1 which is unusual if you run with a water box.
Are you sure the box disintegrates and that is not just an artefact of visualizing the trajectory? Amber doesnt wrap coordinates by default so the raw trajectory looks like it explodes just from diffusion into neighboring boxes. Use ptraj to wrap, center and image your trajectory before analysing.
Kind Regards,
Thomas
On Mon, Mar 18, 2024 at 3:37 PM VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es<mailto:veronica.martin.hernandez.uva.es>> wrote:
Hi Thomas
Thanks for the advice, I am seeing the problem: the water box desintegrates, it's like a water leak in a glass.
do you know how i can solve that problem? because it's my first-time running TI calculations and anyone in my group knows anything about MD.
My input file for the equilibrization is:
TI equilibration
&cntrl
imin = 0,
nstlim = 200,
irest = 0,
ntx = 1,
dt = 0.001,
ntt = 3,
temp0 = 300.0,
gamma_ln = 2.0,
ig = -1,
ntc = 1,
ntf = 1,
ntb = 2, ntp = 1, pres0 = 1.01325, taup = 2.0, barostat = 2
ntwe = 1,
ntwx = 1,
ntpr = 1,
ntwr = 1,
icfe = 1, ifsc = 1, clambda = 0.5, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':408', timask2 = ':409',
scmask1 = '.6559, 6560', scmask2 = '.6588, 6589',
/
&ewald
/
Thanks in advance
Vero
________________________________
De: Steinbrecher, Thomas <thomas.steinbrecher.roche.com<mailto:thomas.steinbrecher.roche.com>>
Enviado: lunes, 18 de marzo de 2024 9:22
Para: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es<mailto:veronica.martin.hernandez.uva.es>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Cc: David A Case <dacase1.gmail.com<mailto:dacase1.gmail.com>>
Asunto: Re: [Sender Not Verified] Re: [AMBER] AMBER error vlimit exceed for step
I recommend running your equilibration for say 100 steps and writing the trajectory at every step (ntwx=1), then visualize what is going wrong, you should see parts of the system entangled or blowing up most likely...
Kind Regards,
Thomas
On Sun, Mar 17, 2024 at 10:54 PM VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
Hi,
Thanks for the advice
The system consists of two proteins and a ligand in a water box of 10 A. To solve the vlimit problem I have tried multiple times to minimize the system and I always have RMS = 2.1066E-03. I have tried setting nstlim=0 for the equilibration step in CPUS (with pmemd) and it doesn't work, I have the following output file:
limit exceeded for step 1; vmax = 32.3673
vlimit exceeded for step 1; vmax = 32.4206
vlimit exceeded for step 1; vmax = 32.8198
vlimit exceeded for step 2; vmax = 24.2420
vlimit exceeded for step 2; vmax = 24.4255
vlimit exceeded for step 2; vmax = 24.2124
vlimit exceeded for step 3; vmax = 29.6206
vlimit exceeded for step 3; vmax = 29.8308
vlimit exceeded for step 3; vmax = 94.4408
vlimit exceeded for step 4; vmax = 29.3028
vlimit exceeded for step 4; vmax = 34.3557
vlimit exceeded for step 4; vmax = 117.7315
vlimit exceeded for step 5; vmax = 27.6234
vlimit exceeded for step 5; vmax = 30.6129
vlimit exceeded for step 5; vmax = **********
vlimit exceeded for step 6; vmax = 25.6441
vlimit exceeded for step 6; vmax = 25.1304
vlimit exceeded for step 6; vmax = **********
vlimit exceeded for step 7; vmax = 307.8461
vlimit exceeded for step 7; vmax = 357.3008
vlimit exceeded for step 7; vmax = 7705.9134
vlimit exceeded for step 8; vmax = 28.8565
vlimit exceeded for step 8; vmax = 42.6049
vlimit exceeded for step 8; vmax = **********
vlimit exceeded for step 9; vmax = 42.6936
vlimit exceeded for step 9; vmax = 149.1554
vlimit exceeded for step 9; vmax = **********
vlimit exceeded for step 10; vmax = 38.8181
vlimit exceeded for step 10; vmax = 330.1020
vlimit exceeded for step 10; vmax = **********
vlimit exceeded for step 11; vmax = 43.6480
vlimit exceeded for step 11; vmax = 233.9341
vlimit exceeded for step 11; vmax = **********
vlimit exceeded for step 12; vmax = 39.6579
vlimit exceeded for step 12; vmax = 109.5508
vlimit exceeded for step 12; vmax = **********
vlimit exceeded for step 13; vmax = 101.4603
vlimit exceeded for step 13; vmax = 216.4174
vlimit exceeded for step 13; vmax = 11938.8945
vlimit exceeded for step 14; vmax = 31.7568
vlimit exceeded for step 14; vmax = 50.4767
vlimit exceeded for step 14; vmax = 29494.5146
vlimit exceeded for step 15; vmax = 37.2987
vlimit exceeded for step 15; vmax = 535.8471
vlimit exceeded for step 15; vmax = **********
vlimit exceeded for step 16; vmax = 39.2310
vlimit exceeded for step 16; vmax = 779.1994
vlimit exceeded for step 16; vmax = **********
vlimit exceeded for step 17; vmax = 85.0499
vlimit exceeded for step 17; vmax = 137.6152
vlimit exceeded for step 17; vmax = **********
vlimit exceeded for step 18; vmax = 35.5123
vlimit exceeded for step 18; vmax = 58.8726
vlimit exceeded for step 18; vmax = 16920.8430
vlimit exceeded for step 19; vmax = 31.6975
vlimit exceeded for step 19; vmax = 169.7575
vlimit exceeded for step 19; vmax = 12849.0825
vlimit exceeded for step 20; vmax = 41.2655
vlimit exceeded for step 20; vmax = 69.7196
vlimit exceeded for step 20; vmax = 62515.7612
vlimit exceeded for step 21; vmax = 43.0620
vlimit exceeded for step 21; vmax = 108.5942
vlimit exceeded for step 21; vmax = **********
vlimit exceeded for step 22; vmax = 55.1685
vlimit exceeded for step 22; vmax = 43.8952
vlimit exceeded for step 22; vmax = 13203.7728
vlimit exceeded for step 23; vmax = 35.5843
vlimit exceeded for step 23; vmax = 48.4065
vlimit exceeded for step 23; vmax = **********
vlimit exceeded for step 24; vmax = 35.8801
vlimit exceeded for step 24; vmax = 69.8332
vlimit exceeded for step 24; vmax = **********
vlimit exceeded for step 25; vmax = 86.3921
vlimit exceeded for step 25; vmax = 47.3555
vlimit exceeded for step 25; vmax = 4326.9551
vlimit exceeded for step 26; vmax = 34.5887
vlimit exceeded for step 26; vmax = 37.7151
vlimit exceeded for step 26; vmax = 14080.5714
vlimit exceeded for step 27; vmax = 31.0572
vlimit exceeded for step 27; vmax = 412.8355
vlimit exceeded for step 27; vmax = 30001.3174
vlimit exceeded for step 28; vmax = 28.3775
vlimit exceeded for step 28; vmax = 42.0237
vlimit exceeded for step 28; vmax = 5940.8854
vlimit exceeded for step 29; vmax = 26.0158
vlimit exceeded for step 29; vmax = 80.0505
vlimit exceeded for step 29; vmax = 12680.8490
vlimit exceeded for step 30; vmax = 28.7866
vlimit exceeded for step 30; vmax = 38.7071
vlimit exceeded for step 30; vmax = 31456.4238
vlimit exceeded for step 31; vmax = 28.3773
vlimit exceeded for step 31; vmax = 35.4634
vlimit exceeded for step 31; vmax = 23000.8525
vlimit exceeded for step 32; vmax = 38.3713
vlimit exceeded for step 32; vmax = 36.4866
vlimit exceeded for step 32; vmax = **********
vlimit exceeded for step 33; vmax = 37.2231
vlimit exceeded for step 33; vmax = 44.2718
vlimit exceeded for step 33; vmax = 12074.8077
vlimit exceeded for step 34; vmax = 33.7451
vlimit exceeded for step 34; vmax = 33.9775
vlimit exceeded for step 34; vmax = 27744.3987
vlimit exceeded for step 35; vmax = 29.3357
vlimit exceeded for step 35; vmax = 82.6470
vlimit exceeded for step 35; vmax = **********
vlimit exceeded for step 36; vmax = 27.0909
vlimit exceeded for step 36; vmax = 38.0134
vlimit exceeded for step 36; vmax = **********
vlimit exceeded for step 37; vmax = 27.3449
vlimit exceeded for step 37; vmax = 85.4464
vlimit exceeded for step 37; vmax = 51928.1135
vlimit exceeded for step 38; vmax = 28.8436
vlimit exceeded for step 38; vmax = 61.2366
vlimit exceeded for step 38; vmax = 21335.5898
vlimit exceeded for step 39; vmax = 29.2573
vlimit exceeded for step 39; vmax = 118.1609
vlimit exceeded for step 39; vmax = 24230.2748
vlimit exceeded for step 40; vmax = 27.0407
vlimit exceeded for step 40; vmax = 42.5681
vlimit exceeded for step 40; vmax = 14509.4245
vlimit exceeded for step 41; vmax = 29.3425
vlimit exceeded for step 41; vmax = 37.1298
vlimit exceeded for step 41; vmax = 15447.5533
vlimit exceeded for step 42; vmax = 30.0402
vlimit exceeded for step 42; vmax = 46.5200
vlimit exceeded for step 42; vmax = 99028.4276
vlimit exceeded for step 43; vmax = 27.2300
vlimit exceeded for step 43; vmax = 61.1055
vlimit exceeded for step 43; vmax = 17553.5221
vlimit exceeded for step 44; vmax = 27.9962
vlimit exceeded for step 44; vmax = 213.7720
vlimit exceeded for step 44; vmax = 99712.8070
vlimit exceeded for step 45; vmax = 26.0071
vlimit exceeded for step 45; vmax = 112.6361
vlimit exceeded for step 45; vmax = **********
vlimit exceeded for step 46; vmax = 27.1267
vlimit exceeded for step 46; vmax = 37.1819
vlimit exceeded for step 46; vmax = 67261.3482
vlimit exceeded for step 47; vmax = 27.0349
vlimit exceeded for step 47; vmax = 38.5739
vlimit exceeded for step 47; vmax = 27802.3618
vlimit exceeded for step 48; vmax = 27.5764
vlimit exceeded for step 48; vmax = 95.1639
vlimit exceeded for step 48; vmax = 40189.4135
vlimit exceeded for step 49; vmax = 24.6853
vlimit exceeded for step 49; vmax = 111.6050
vlimit exceeded for step 49; vmax = **********
vlimit exceeded for step 50; vmax = 25.8712
vlimit exceeded for step 50; vmax = 52.7314
vlimit exceeded for step 50; vmax = **********
vlimit exceeded for step 51; vmax = 57.6060
vlimit exceeded for step 51; vmax = 55.4552
vlimit exceeded for step 51; vmax = **********
vlimit exceeded for step 52; vmax = 27.0312
vlimit exceeded for step 52; vmax = 30.8076
vlimit exceeded for step 52; vmax = 69149.2287
vlimit exceeded for step 53; vmax = 37.0875
vlimit exceeded for step 53; vmax = 45.6289
vlimit exceeded for step 53; vmax = 28161.3233
vlimit exceeded for step 54; vmax = 27.0844
vlimit exceeded for step 54; vmax = 50.1372
vlimit exceeded for step 54; vmax = 25351.6244
vlimit exceeded for step 55; vmax = 27.1160
vlimit exceeded for step 55; vmax = 35.2034
vlimit exceeded for step 55; vmax = **********
vlimit exceeded for step 56; vmax = 26.3764
vlimit exceeded for step 56; vmax = 120.9395
vlimit exceeded for step 56; vmax = **********
vlimit exceeded for step 57; vmax = 29.5180
vlimit exceeded for step 57; vmax = 245.9346
vlimit exceeded for step 57; vmax = **********
vlimit exceeded for step 58; vmax = 25.6729
vlimit exceeded for step 58; vmax = 46.6015
vlimit exceeded for step 58; vmax = 60669.6452
vlimit exceeded for step 59; vmax = 362.5738
vlimit exceeded for step 59; vmax = 53.4425
vlimit exceeded for step 59; vmax = 15033.0079
vlimit exceeded for step 60; vmax = 61.9380
vlimit exceeded for step 60; vmax = 63.8230
vlimit exceeded for step 60; vmax = **********
vlimit exceeded for step 61; vmax = 8123.6906
vlimit exceeded for step 61; vmax = 214.3276
vlimit exceeded for step 61; vmax = 29747.1497
vlimit exceeded for step 62; vmax = 2101.3458
vlimit exceeded for step 62; vmax = 36.3414
vlimit exceeded for step 62; vmax = 30020.9834
vlimit exceeded for step 63; vmax = 293.7447
vlimit exceeded for step 63; vmax = 38.1398
vlimit exceeded for step 63; vmax = **********
vlimit exceeded for step 64; vmax = 1989.1673
vlimit exceeded for step 64; vmax = 63.1038
vlimit exceeded for step 64; vmax = 18469.4221
vlimit exceeded for step 65; vmax = 466.6967
vlimit exceeded for step 65; vmax = 39.2645
vlimit exceeded for step 65; vmax = 2432.7444
vlimit exceeded for step 66; vmax = 487.8643
vlimit exceeded for step 66; vmax = 39.6814
vlimit exceeded for step 66; vmax = **********
vlimit exceeded for step 67; vmax = 10489.8336
vlimit exceeded for step 67; vmax = 37.0926
vlimit exceeded for step 67; vmax = 13694.0859
vlimit exceeded for step 68; vmax = 1668.0066
vlimit exceeded for step 68; vmax = 40.2146
vlimit exceeded for step 68; vmax = **********
vlimit exceeded for step 69; vmax = 423.4574
vlimit exceeded for step 69; vmax = 38.9409
vlimit exceeded for step 69; vmax = **********
vlimit exceeded for step 70; vmax = 261.9830
vlimit exceeded for step 70; vmax = 35.5942
vlimit exceeded for step 70; vmax = **********
vlimit exceeded for step 71; vmax = 1306.8247
vlimit exceeded for step 71; vmax = 33.8907
vlimit exceeded for step 71; vmax = 66528.4669
vlimit exceeded for step 72; vmax = 476.8872
vlimit exceeded for step 72; vmax = 31.1395
vlimit exceeded for step 72; vmax = 5526.9385
vlimit exceeded for step 73; vmax = 260.9138
vlimit exceeded for step 73; vmax = 29.7000
vlimit exceeded for step 73; vmax = **********
vlimit exceeded for step 74; vmax = 192.9928
vlimit exceeded for step 74; vmax = 49.0064
vlimit exceeded for step 74; vmax = 68451.1562
vlimit exceeded for step 75; vmax = 163.2315
vlimit exceeded for step 75; vmax = 71.3741
vlimit exceeded for step 75; vmax = 49665.1892
vlimit exceeded for step 76; vmax = 348.5080
vlimit exceeded for step 76; vmax = 303.1682
vlimit exceeded for step 76; vmax = 22275.8971
vlimit exceeded for step 77; vmax = 182.2261
vlimit exceeded for step 77; vmax = 33.9435
vlimit exceeded for step 77; vmax = 30088.3638
vlimit exceeded for step 78; vmax = 100.5298
vlimit exceeded for step 78; vmax = 49.0988
vlimit exceeded for step 78; vmax = **********
vlimit exceeded for step 79; vmax = 123.8449
vlimit exceeded for step 79; vmax = 35.3065
vlimit exceeded for step 79; vmax = **********
vlimit exceeded for step 80; vmax = 867.9408
vlimit exceeded for step 80; vmax = 40.1668
vlimit exceeded for step 80; vmax = 6095.2668
vlimit exceeded for step 81; vmax = 164.5995
vlimit exceeded for step 81; vmax = 47.9888
vlimit exceeded for step 81; vmax = 67651.5280
vlimit exceeded for step 82; vmax = 142.8634
vlimit exceeded for step 82; vmax = 39.3408
vlimit exceeded for step 82; vmax = **********
vlimit exceeded for step 83; vmax = 280.2824
vlimit exceeded for step 83; vmax = 32.3403
vlimit exceeded for step 83; vmax = 14722.0120
vlimit exceeded for step 84; vmax = 495.9626
vlimit exceeded for step 84; vmax = 442.0213
vlimit exceeded for step 84; vmax = 11532.5253
vlimit exceeded for step 85; vmax = 107.7909
vlimit exceeded for step 85; vmax = 58.8003
vlimit exceeded for step 85; vmax = 54204.3087
vlimit exceeded for step 86; vmax = 166.1315
vlimit exceeded for step 86; vmax = 58.3265
vlimit exceeded for step 86; vmax = **********
vlimit exceeded for step 87; vmax = 171.0298
vlimit exceeded for step 87; vmax = 387.4200
vlimit exceeded for step 87; vmax = 22967.0792
vlimit exceeded for step 88; vmax = 148.1763
vlimit exceeded for step 88; vmax = 55.1111
vlimit exceeded for step 88; vmax = **********
vlimit exceeded for step 89; vmax = 69.2086
vlimit exceeded for step 89; vmax = 210.1151
vlimit exceeded for step 89; vmax = **********
vlimit exceeded for step 90; vmax = 1053.2048
vlimit exceeded for step 90; vmax = 1069.1222
vlimit exceeded for step 90; vmax = **********
vlimit exceeded for step 91; vmax = 119.9532
vlimit exceeded for step 91; vmax = 45.4942
vlimit exceeded for step 91; vmax = **********
vlimit exceeded for step 92; vmax = 413.0896
vlimit exceeded for step 92; vmax = 60.5829
vlimit exceeded for step 92; vmax = **********
vlimit exceeded for step 93; vmax = 487.2212
vlimit exceeded for step 93; vmax = 235.2823
vlimit exceeded for step 93; vmax = **********
vlimit exceeded for step 94; vmax = 146.6982
vlimit exceeded for step 94; vmax = 79.9670
vlimit exceeded for step 94; vmax = **********
vlimit exceeded for step 95; vmax = 431.7458
vlimit exceeded for step 95; vmax = 159.9780
vlimit exceeded for step 95; vmax = **********
vlimit exceeded for step 96; vmax = 193.6649
vlimit exceeded for step 96; vmax = 43.3442
vlimit exceeded for step 96; vmax = **********
vlimit exceeded for step 97; vmax = 880.1310
vlimit exceeded for step 97; vmax = 49.6749
vlimit exceeded for step 97; vmax = **********
vlimit exceeded for step 98; vmax = 128.7707
vlimit exceeded for step 98; vmax = 45.0238
vlimit exceeded for step 98; vmax = **********
vlimit exceeded for step 99; vmax = 98.3865
vlimit exceeded for step 99; vmax = 63.9347
vlimit exceeded for step 99; vmax = 64042.0568
vlimit exceeded for step 100; vmax = 151.4353
vlimit exceeded for step 100; vmax = 45.8228
vlimit exceeded for step 100; vmax = **********
vlimit exceeded for step 101; vmax = 48.7788
vlimit exceeded for step 101; vmax = 51.6213
vlimit exceeded for step 101; vmax = **********
vlimit exceeded for step 102; vmax = 135.9853
vlimit exceeded for step 102; vmax = 54.9482
vlimit exceeded for step 102; vmax = **********
vlimit exceeded for step 103; vmax = 259.7308
vlimit exceeded for step 103; vmax = 77.6798
vlimit exceeded for step 103; vmax = **********
vlimit exceeded for step 104; vmax = 191.6293
vlimit exceeded for step 104; vmax = 41.7407
vlimit exceeded for step 104; vmax = 80019.7567
vlimit exceeded for step 105; vmax = 250.0711
vlimit exceeded for step 105; vmax = 704.1223
vlimit exceeded for step 105; vmax = **********
vlimit exceeded for step 106; vmax = 130.3092
vlimit exceeded for step 106; vmax = 51.4611
vlimit exceeded for step 106; vmax = **********
vlimit exceeded for step 107; vmax = 268.4482
vlimit exceeded for step 107; vmax = 51.2162
vlimit exceeded for step 107; vmax = **********
vlimit exceeded for step 108; vmax = 102.9668
vlimit exceeded for step 108; vmax = 33.7432
vlimit exceeded for step 108; vmax = **********
vlimit exceeded for step 109; vmax = 60.6987
vlimit exceeded for step 109; vmax = 79.9954
vlimit exceeded for step 109; vmax = 10822.8863
vlimit exceeded for step 110; vmax = 213.4419
vlimit exceeded for step 110; vmax = 87.1096
vlimit exceeded for step 110; vmax = 46653.8800
vlimit exceeded for step 111; vmax = 242.8401
vlimit exceeded for step 111; vmax = 77.7780
vlimit exceeded for step 111; vmax = **********
vlimit exceeded for step 112; vmax = 91.3156
vlimit exceeded for step 112; vmax = 144.8750
vlimit exceeded for step 112; vmax = **********
vlimit exceeded for step 113; vmax = 54.7847
vlimit exceeded for step 113; vmax = 35.0237
vlimit exceeded for step 113; vmax = **********
vlimit exceeded for step 114; vmax = 691.8938
vlimit exceeded for step 114; vmax = 686.5649
vlimit exceeded for step 114; vmax = **********
vlimit exceeded for step 115; vmax = 450.3385
vlimit exceeded for step 115; vmax = 34.7856
vlimit exceeded for step 115; vmax = **********
vlimit exceeded for step 116; vmax = 180.3758
vlimit exceeded for step 116; vmax = 95.4283
vlimit exceeded for step 116; vmax = **********
vlimit exceeded for step 117; vmax = 51.9801
vlimit exceeded for step 117; vmax = 64.8389
vlimit exceeded for step 117; vmax = **********
vlimit exceeded for step 118; vmax = 62.6499
vlimit exceeded for step 118; vmax = 240.1318
vlimit exceeded for step 118; vmax = **********
vlimit exceeded for step 119; vmax = 46.0877
vlimit exceeded for step 119; vmax = 127.7745
vlimit exceeded for step 119; vmax = 36645.7161
vlimit exceeded for step 120; vmax = 200.5976
vlimit exceeded for step 120; vmax = 53.1126
vlimit exceeded for step 120; vmax = **********
vlimit exceeded for step 121; vmax = 179.0600
vlimit exceeded for step 121; vmax = 40.2410
vlimit exceeded for step 121; vmax = **********
vlimit exceeded for step 122; vmax = 106.2868
vlimit exceeded for step 122; vmax = 113.7540
vlimit exceeded for step 122; vmax = **********
vlimit exceeded for step 123; vmax = 209.5541
vlimit exceeded for step 123; vmax = 38.6516
vlimit exceeded for step 123; vmax = **********
vlimit exceeded for step 124; vmax = 100.9789
vlimit exceeded for step 124; vmax = 383.3916
vlimit exceeded for step 124; vmax = **********
vlimit exceeded for step 125; vmax = 70.2286
vlimit exceeded for step 125; vmax = 41.3917
vlimit exceeded for step 125; vmax = **********
vlimit exceeded for step 126; vmax = 42.3924
vlimit exceeded for step 126; vmax = 80.1591
vlimit exceeded for step 126; vmax = 41023.2229
vlimit exceeded for step 127; vmax = 160.7358
vlimit exceeded for step 127; vmax = 88.6361
vlimit exceeded for step 127; vmax = 68808.7963
vlimit exceeded for step 128; vmax = 123.8464
vlimit exceeded for step 128; vmax = 41.8218
vlimit exceeded for step 128; vmax = **********
vlimit exceeded for step 129; vmax = 91.8765
vlimit exceeded for step 129; vmax = 58.1055
vlimit exceeded for step 129; vmax = 98658.8478
vlimit exceeded for step 130; vmax = 210.5586
vlimit exceeded for step 130; vmax = 53.2877
vlimit exceeded for step 130; vmax = **********
vlimit exceeded for step 131; vmax = 212.5414
vlimit exceeded for step 131; vmax = 43.2532
vlimit exceeded for step 131; vmax = 20002.5951
vlimit exceeded for step 132; vmax = 42.7361
vlimit exceeded for step 132; vmax = 98.3046
vlimit exceeded for step 132; vmax = **********
vlimit exceeded for step 133; vmax = 75.2493
vlimit exceeded for step 133; vmax = 48.1182
vlimit exceeded for step 133; vmax = 34014.4997
vlimit exceeded for step 134; vmax = 50.2791
vlimit exceeded for step 134; vmax = 55.8910
vlimit exceeded for step 134; vmax = **********
vlimit exceeded for step 135; vmax = 142.3634
vlimit exceeded for step 135; vmax = 44.7872
vlimit exceeded for step 135; vmax = **********
vlimit exceeded for step 136; vmax = 174.0444
vlimit exceeded for step 136; vmax = 37.5359
vlimit exceeded for step 136; vmax = 46024.0561
vlimit exceeded for step 137; vmax = 99.5935
vlimit exceeded for step 137; vmax = 33.8032
vlimit exceeded for step 137; vmax = **********
vlimit exceeded for step 138; vmax = 123.3957
vlimit exceeded for step 138; vmax = 42.6069
vlimit exceeded for step 138; vmax = 38170.5451
vlimit exceeded for step 139; vmax = 624.3686
vlimit exceeded for step 139; vmax = 106.5963
vlimit exceeded for step 139; vmax = **********
vlimit exceeded for step 140; vmax = 1890.9990
vlimit exceeded for step 140; vmax = 60.4480
vlimit exceeded for step 140; vmax = **********
vlimit exceeded for step 141; vmax = 99.4308
vlimit exceeded for step 141; vmax = 32.6046
vlimit exceeded for step 141; vmax = **********
vlimit exceeded for step 142; vmax = 43.0531
vlimit exceeded for step 142; vmax = 39.9058
vlimit exceeded for step 142; vmax = 48154.6678
vlimit exceeded for step 143; vmax = 81.5598
vlimit exceeded for step 143; vmax = 46.8248
vlimit exceeded for step 143; vmax = **********
vlimit exceeded for step 144; vmax = 82.1984
vlimit exceeded for step 144; vmax = 37.3271
vlimit exceeded for step 144; vmax = **********
vlimit exceeded for step 145; vmax = 79.8786
vlimit exceeded for step 145; vmax = 44.0806
vlimit exceeded for step 145; vmax = **********
vlimit exceeded for step 146; vmax = 44.6117
vlimit exceeded for step 146; vmax = 41.9424
vlimit exceeded for step 146; vmax = **********
vlimit exceeded for step 147; vmax = 45.4977
vlimit exceeded for step 147; vmax = 38.4046
vlimit exceeded for step 147; vmax = **********
vlimit exceeded for step 148; vmax = 42.5670
vlimit exceeded for step 148; vmax = 33.9638
vlimit exceeded for step 148; vmax = **********
vlimit exceeded for step 149; vmax = 125.3138
vlimit exceeded for step 149; vmax = 54.7060
vlimit exceeded for step 149; vmax = **********
vlimit exceeded for step 150; vmax = 39.9070
vlimit exceeded for step 150; vmax = 34.3443
vlimit exceeded for step 150; vmax = **********
vlimit exceeded for step 151; vmax = 70.8209
vlimit exceeded for step 151; vmax = 38.9678
vlimit exceeded for step 151; vmax = **********
vlimit exceeded for step 152; vmax = 47.0263
vlimit exceeded for step 152; vmax = 26.7370
vlimit exceeded for step 152; vmax = 59709.1619
vlimit exceeded for step 153; vmax = 69.2901
vlimit exceeded for step 153; vmax = 48.4906
vlimit exceeded for step 153; vmax = **********
vlimit exceeded for step 154; vmax = 52.0409
vlimit exceeded for step 154; vmax = 42.4747
vlimit exceeded for step 154; vmax = **********
vlimit exceeded for step 155; vmax = 132.1344
vlimit exceeded for step 155; vmax = 34.5602
vlimit exceeded for step 155; vmax = **********
vlimit exceeded for step 156; vmax = 74.3201
vlimit exceeded for step 156; vmax = 34.1045
vlimit exceeded for step 156; vmax = **********
vlimit exceeded for step 157; vmax = 314.3385
vlimit exceeded for step 157; vmax = 33.8375
vlimit exceeded for step 157; vmax = **********
vlimit exceeded for step 158; vmax = 48.6327
vlimit exceeded for step 158; vmax = 30.8204
vlimit exceeded for step 158; vmax = **********
vlimit exceeded for step 159; vmax = 36.7491
vlimit exceeded for step 159; vmax = 29.1226
vlimit exceeded for step 159; vmax = **********
vlimit exceeded for step 160; vmax = 50.1280
vlimit exceeded for step 160; vmax = 31.5635
vlimit exceeded for step 160; vmax = **********
vlimit exceeded for step 161; vmax = 228.8995
vlimit exceeded for step 161; vmax = 30.2455
vlimit exceeded for step 161; vmax = **********
vlimit exceeded for step 162; vmax = 50.8843
vlimit exceeded for step 162; vmax = 29.7989
vlimit exceeded for step 162; vmax = 11749.7172
vlimit exceeded for step 163; vmax = 44.1582
vlimit exceeded for step 163; vmax = 33.2180
vlimit exceeded for step 163; vmax = **********
vlimit exceeded for step 164; vmax = 36.9590
vlimit exceeded for step 164; vmax = 30.4480
vlimit exceeded for step 164; vmax = 14231.5372
vlimit exceeded for step 165; vmax = 219.4613
vlimit exceeded for step 165; vmax = 28.6193
vlimit exceeded for step 165; vmax = 48063.1971
vlimit exceeded for step 166; vmax = 468.9978
vlimit exceeded for step 166; vmax = 201.0577
vlimit exceeded for step 166; vmax = **********
So, I don't know how I should solve the problem, but I appreciate every help
Thanks in advance
Vero
________________________________
De: David A Case <dacase1.gmail.com<mailto:dacase1.gmail.com>>
Enviado: miércoles, 13 de marzo de 2024 17:04
Para: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es<mailto:veronica.martin.hernandez.uva.es>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Asunto: Re: [AMBER] AMBER error vlimit exceed for step
On Fri, Mar 08, 2024, VERONICA MARTIN HERNANDEZ via AMBER wrote:
>
>I was performing TI calculations and the minimization went well,
>But when I perform the equilibration step (I do it with pmemd and cpus) I
>have always got the error of vlimit exceed for step, even from step 0.
Run a zero-step (nstlim=0) MD equilibration run, and very carefully check
the differences in energy between the first step and the final step of
minimization. (It is often the case the people turn off SHAKE for
minimization, but turn it back on for MD: that *could* be a the origin of
your problem, but I'm just guessing here: you need to do some detective work
on your end.)
...good luck...dac
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Dr. Thomas Steinbrecher
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
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Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com<mailto:thomas.steinbrecher.roche.com>
--
Dr. Thomas Steinbrecher
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com<mailto:thomas.steinbrecher.roche.com>
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Received on Wed Mar 20 2024 - 04:30:02 PDT
