From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri May 12 2017 - 13:41:54 CDT
Hi!
the eABF seems promising as well
http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b10055
Does it work one more complex systems as well?
Best,
Ajasja
On 12 May 2017 at 20:29, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:
> Thanks! I'll try the metadynamics approach then
>
> On Fri, May 12, 2017 at 9:43 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Sebastian, the tilt variable does not support total force calculations:
>>
>> http://colvars.github.io/colvars-refman-namd/colvars-refman-
>> namd.html#x1-530005.3.3
>>
>> so you can either use one of the existing eABF implementations, or
>> alternatively, metadynamics, umbrella sampling, etc
>>
>> Giacomo
>>
>> On Fri, May 12, 2017 at 9:34 AM, The Cromicus Productions <
>> thecromicusproductions_at_gmail.com> wrote:
>>
>>> Hi everyone,
>>>
>>> I'm trying to do ABF on two collective variables but the tilt one is
>>> giving me the following
>>> errors:
>>> colvars: No dependency satisfied among alternates:
>>> colvars: -----------------------------------------
>>> colvars: 1. extended Lagrangian
>>> colvars: Feature unavailable: "extended Lagrangian" in colvar
>>> TiltAngle
>>> colvars: 2. total force calculation
>>> colvars: Feature unavailable: "Jacobian derivative" in cvc
>>> tilt0001
>>> colvars: ...required by "Jacobian derivative" in colvar TiltAngle
>>> colvars: ...required by "total force calculation" in colvar
>>> TiltAngle
>>> colvars: -----------------------------------------
>>> colvars: for "total force" in colvar TiltAngle
>>> colvars: ...required by "obtain total force" in bias abf1
>>> colvars: Error: Failed dependency in bias abf1.
>>> FATAL ERROR: Error in the collective variables module: exiting.
>>>
>>> This is my definition of the collective variables. Any idea of what am I
>>> doing wrong?
>>> Thanks you very much!
>>>
>>> colvarsTrajFrequency 500
>>> colvarsRestartFrequency 20000
>>>
>>> colvar {
>>> name NormalMolMem
>>>
>>> width 0.05
>>>
>>> lowerBoundary 3
>>> lowerWallConstant 20.0
>>> upperBoundary 15
>>> upperWallConstant 20.0
>>>
>>> outputValue
>>> outputAppliedForce
>>>
>>> distanceZ {
>>> main {
>>> atomNumbers { 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163
>>> 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178
>>> 1179 1180 1181 }
>>> }
>>> ref {
>>> atomNumbers { 6 8 14 16 22 24 30 32 38 40 46 48 54 56 62 64 70 72 78 80
>>> 86 88 94 96 102 104 110 112 118 120 126 128 134 136 142 144 150 152 158 160
>>> 166 168 174 176 182 184 190 192 198 200 206 208 214 216 222 224 230 232 238
>>> 240 246 248 254 256 262 264 270 272 278 280 286 288 294 296 302 304 310 312
>>> 318 320 326 328 334 336 342 344 350 352 358 360 366 368 374 376 382 384 390
>>> 392 398 400 406 408 414 416 422 424 430 432 438 440 446 448 454 456 462 464
>>> 470 472 478 480 486 488 494 496 502 504 510 512 518 520 526 528 534 536 542
>>> 544 550 552 558 560 566 568 574 576 582 584 590 592 598 600 606 608 614 616
>>> 622 624 630 632 638 640 646 648 654 656 662 664 670 672 678 680 686 688 694
>>> 696 702 704 710 712 718 720 726 728 734 736 742 744 750 752 758 760 766 768
>>> 774 776 782 784 790 792 798 800 806 808 814 816 822 824 830 832 838 840 846
>>> 848 854 856 862 864 870 872 878 880 886 888 894 896 902 904 910 912 918 920
>>> 926 928 934 936 942 944 950 952 958 960 966 968 974 976 982 984 990 992 998
>>> 1000 1006 1008 1014 1016 1022 1024 1030 1032 1038 1040 1046 1048 1054 1056
>>> 1062 1064 1070 1072 1078 1080 1086 1088 1094 1096 1102 1104 1110 1112 1118
>>> 1120 1126 1128 1134 1136 1142 1144 1150 1152 }
>>> }
>>> }
>>> }
>>>
>>> colvar {
>>> name TiltAngle
>>>
>>> width 0.05
>>>
>>> lowerBoundary -1
>>> lowerWallConstant 20.0
>>> upperBoundary 1
>>> upperWallConstant 20.0
>>>
>>> tilt {
>>> atoms {
>>> atomNumbers { 1162 1163 1165 1167 1169 1170 }
>>> }
>>> refPositions {
>>> (2.128,-7.221,-2.489) (3.177,-9.110,-2.489) (1.837,-10.595,-2.489)
>>> (3.561,-12.419,-2.489) (4.828,-7.499,-2.489) (5.536,-9.607,-2.489)
>>> }
>>> }
>>> }
>>>
>>>
>>>
>>>
>>> abf {
>>> colvars NormalMolMem TiltAngle
>>> fullSamples 500
>>> historyFreq 20000
>>> }
>>>
>>>
>>> -------------------------------------
>>> Sebastian
>>>
>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
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