From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon May 15 2017 - 08:42:37 CDT
Hi,
I can only second what Giacomo said. Ultimately, the hard part is dealing
with slow degrees of freedom that couple to your chosen coordinate(s). That
is handled in a very similar way by ABF and eABF. In difficult cases, there
are often multiple pathways, then the multiple-walker versions can be quite
effective.
Jerome
On 12 May 2017 at 21:00, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
> 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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