From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 12 2017 - 14:00:25 CDT
Hi Ajasja, Jérôme can elaborate on the details, but you should definitely
try for your system. If a method converges formally in the limit of large
sampling, a more "complex system" is supported out of the box.
The only complication of eABF compared to other methods is the presence of
the gap between "actual" and "extended" values of the variable. That gap
will average out to zero, and each estimator will make different
assumptions on its distribution (see papers for details). For sure,
though, the central limit theorem will help.
Ultimately, it is the correlation time of the "true" variable that will
most affect the rate of integration over the "gap" variable vs. the rate at
which the whole PMF is reconstructed.
Giacomo
On Fri, May 12, 2017 at 2:41 PM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
wrote:
> 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
>>>
>>
>>
>
-- 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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