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#36981 - 05/23/18 11:24 PM CHARMM 39b2: maximum number of table atoms exceeded
rongzhenliao Offline
Forum Member

Registered: 06/16/16
Posts: 1
Hi,
I used a 60 angstrom water droplet to solvate my system.
I used the following for my solvent boundary potential:
sbound set xref 0.0 yref 0.0 zref 0.0 assign 1 sele ((resn TIP3 -
.and. type oh2)) end
and get the following error:
SELRPN> 29110 atoms have been selected out of 87393
***** LEVEL -1 WARNING FROM MKALIS *****
***** maximum number of table atoms exceeded
******************************************
BOMLEV ( -1) IS REACHED - TERMINATING. WRNLEV IS 5
I used Charmm version 39b2, which can treat "Maximum number of ATOMS:360720, and RESidues:120240". I found some suggestion from previous post:
"increase NMCATM = 12000 to something bigger in c33b2/source/fcm/dimens.fcm"
However, I could not find related file in Charmm version 39b2. Any suggestion to solve this problem? Thank you very much.

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#36982 - 05/24/18 12:44 PM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rongzhenliao]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8336
Loc: 39 03 48 N, 77 06 54 W
See doc/dimens.doc
_________________________
Rick Venable
computational chemist


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#37441 - 03/27/19 09:08 PM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rongzhenliao]
tyrion_jj Offline
Forum Member

Registered: 01/08/19
Posts: 19
Hi,
Do you solve this problem now? Can you tell me what the command you increase? Thanks a lot! I increase "dimension chsize 900000" but the warning ("maximum number of table atoms exceeded") still exist.


Edited by tyrion_jj (03/27/19 09:10 PM)

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#37443 - 03/28/19 03:26 AM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rongzhenliao]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4724
Loc: ~ 59N, 15E
The file you need to change is source/ltm/dimens_ltm.src and then issue the same install.com command as when CHARMM was installed.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37444 - 03/28/19 04:46 AM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: lennart]
tyrion_jj Offline
Forum Member

Registered: 01/08/19
Posts: 19
Hi lennart,
I follow your indication. And my charmm version is 42b2. Firstly, I modify the ../charmm/source/ltm/dimens_ltm.src (" NMCATM = 999999"). Then, I backed to the ../charmm file and performed command "./install.com gnu M". But the error still exit. Where was my performence wrong? Thanks a lot for your replying.

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#37445 - 03/28/19 05:27 AM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rongzhenliao]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4724
Loc: ~ 59N, 15E
What does the logfile tell you when you re-install CHARMM? It may be that it did not actually do anything. You may try
install.com gnu M distclean (which removes the build, lib and exec directories)
followed by
install.com gnu M
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37446 - 03/28/19 06:21 AM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: lennart]
tyrion_jj Offline
Forum Member

Registered: 01/08/19
Posts: 19
Hi lennart,
I really thank you for taking your time to reply me. I follow your suggestion, but my problem still exit. And then I delete the charmm file, and next re-extract (tar -xvf charmm.tar.gz) the "charmm.tar.gz" file, and then, as before, I modify the ../charmm/source/ltm/dimens_ltm.src (NMCATM = 99999). Then, I went back to the ../charmm file and performed command "./install.com gnu M". But my outfile still wrong as below:
------
sbound set xref 0.0 yref 0.0 zref 0.0 assign 1 -
CHARMM> sele resname TIP3 .and. type OH2 .or. resname SOD end
SELRPN> 22841 atoms have been selected out of 83980

***** LEVEL -1 WARNING FROM MKALIS *****
***** maximum number of table atoms exceeded
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5


***** LEVEL -1 WARNING FROM MKALIS *****
***** maximum number of table atoms exceeded
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5
-----

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#37447 - 03/28/19 03:08 PM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rongzhenliao]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8336
Loc: 39 03 48 N, 77 06 54 W
The error message suggests either a problem with your build process, or that you are using a different executable than the one you just built to run your script.
_________________________
Rick Venable
computational chemist


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#37448 - 03/29/19 02:48 AM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rmv]
tyrion_jj Offline
Forum Member

Registered: 01/08/19
Posts: 19
Hi Rick,
Thank you so much for helping me. I set sbound by using a .pot file as below:
--------------------------------------------
* TIP3P DEFORMABLE BOUNDARY POTENTIAL FOR A SPHERE
* COMPUTED FOR 36.80 A RADIUS (RCUT = 7.50)
* CREATED BY C.L. Brooks III from ws-sbmd on Thu Apr 26 04:07:37 2012
*
ROWS 98 COLUmns 5
COLUmn 1 radius
COLUmn 2 potential
COLUmn 3 spline C1
COLUmn 4 spline C2
COLUmn 5 spline C3
29.2682 0 -2.4204517e-13 3.921131754e-12 -1.411607432e-11
29.36079259 0 1.21022585e-13 5.452606577e-28 -1.411607432e-11
29.45338519 0 -2.4204517e-13 -3.921131754e-12 7.058037158e-11
29.54597778 0 8.471580951e-13 1.568452702e-11 -2.68205412e-10
29.63857037 0 -3.14658721e-12 -5.881697632e-11 1.002241276e-09
29.73116296 0 1.173919075e-11 2.195833783e-10 -3.740759694e-09
29.82375556 0 -4.381017578e-11 -8.195165367e-10 1.39607975e-08
29.91634815 0 1.635015124e-10 3.058482768e-09 -5.21024303e-08
30.00894074 0 -6.101958736e-10 -1.141441454e-08 1.944489237e-07
30.10153333 0 2.277281982e-09 4.259917538e-08 -7.256932645e-07
30.19412593 0 -8.498932055e-09 -1.58982287e-07 2.708324134e-06
30.28671852 0 3.171844624e-08 5.933299726e-07 -1.010760327e-05
30.37931111 0 -1.183748529e-07 -2.214337603e-06 3.772208896e-05
30.4719037 0 4.417809654e-07 8.26402044e-06 -0.0001407807526
30.5644963 0 -1.648749009e-06 -3.084174416e-05 0.0005254009213
30.65708889 0 6.153215069e-06 0.0001151029562 -0.001960822933
30.74968148 0 -2.296411127e-05 -0.0004295700806 -0.00535188233
30.84227407 -1.00576744e-05 -0.0002401654207 -0.001916204061 -0.006442696629
30.93486667 -5.383799495e-05 -0.0007607252425 -0.003705842014 -0.00850565462
31.02745926 -0.0001627992025 -0.001665759119 -0.006068523853 -0.009800308129
31.12005185 -0.0003768437693 -0.003041625371 -0.008790831666 -0.006992188313
31.21264444 -0.0007393935851 -0.004849397395 -0.0107331062 -0.0189764058
31.30523704 -0.001295495031 -0.007325085935 -0.01600433003 0.009731094247
31.39782963 -0.002103230207 -0.01003856541 -0.0133012483 -0.01529788708
31.49042222 -0.003158907725 -0.01289522371 -0.01755066137 -0.03105571655
31.58301481 -0.004528031583 -0.01694410433 -0.0261772493 0.01597668948
31.67560741 -0.006308675041 -0.02138082001 -0.02173928 -0.03261190784
31.7682 -0.008500648268 -0.02624539624 -0.03079814329 -0.00759274704
31.86079259 -0.01120084936 -0.03214404281 -0.03290723969 -0.01828897427
31.95338519 -0.01447379453 -0.03870837152 -0.03798751032 -0.01717910928
32.04597778 -0.01839722201 -0.04618494517 -0.04275948512 -0.0163954162
32.13857037 -0.0230532147 -0.05452506114 -0.0473137674 -0.02474486308
32.23116296 -0.02852711404 -0.06392331187 -0.05418734048 -0.01419976534
32.32375556 -0.03492178055 -0.07432322486 -0.05813171974 -0.04406791205
32.41634815 -0.04233692896 -0.08622179209 -0.07037280642 0.01075720471
32.50894074 -0.0509152222 -0.09897711621 -0.067384694 -0.05879433558
32.60153333 -0.06070415797 -0.1129679632 -0.08371645388 -0.02445887152
32.69412593 -0.07190130447 -0.1291000964 -0.09051058486 -0.002691313414
32.78671852 -0.08463313593 -0.1459305369 -0.09125817192 -0.03506125715
32.87931111 -0.09895544717 -0.1637319797 -0.10099741 -0.02790778062
32.9719037 -0.1150038598 -0.1831529965 -0.1087495713 -0.01581760992
33.0644963 -0.1329073794 -0.2036986375 -0.1131433518 0.02482191227
33.15708889 -0.1527186818 -0.2240126864 -0.1062483762 -0.0368872237
33.24968148 -0.174400788 -0.2446370571 -0.1164948272 0.02575126599
33.34227407 -0.1980306806 -0.2655478464 -0.1093416978 0.08905234787
33.43486667 -0.2234851803 -0.2835058679 -0.08460493449 0.09503348046
33.52745926 -0.2503856339 -0.2967291716 -0.05820674548 0.1799113039
33.62005185 -0.2782167669 -0.3028808502 -0.008231383278 0.358307534
33.71264444 -0.3060474248 -0.2951894517 0.09129848728 0.7110555976
33.80523704 -0.3320325852 -0.2599938574 0.2888139311 1.378216104
33.89782963 -0.3525359042 -0.171061851 0.6716517377 3.377904345
33.99042222 -0.359935144 0.04019835617 1.6099585 6.115168762
34.08301481 -0.3375558567 0.4956219663 3.30861649 10.65525005
34.17560741 -0.2548403993 1.382383509 6.268408171 2.692512454
34.2682 -0.07096302635 2.6124517 7.016328297 -12.44136105
34.36079259 0.2212080023 3.591777901 3.560394672 4.344134553
34.45338519 0.58775319 4.362842104 4.767098714 9.41386113
34.54597778 1.040063266 5.48776422 7.382060139 -15.70637943
34.63857037 1.599010619 6.450841729 3.019176965 4.118633073
34.73116296 2.225464859 7.115880495 4.163241707 9.610479408
34.82375556 2.927664879 8.134034294 6.83281932 -23.67015151
34.91634815 3.720606485 8.790571012 0.2577772351 3.080400908
35.00894074 4.539203592 8.917535955 1.113444154 26.28339792
35.10153333 5.395311963 9.799742638 8.414388019 -17.01018669
35.19412593 6.361332121 10.92045784 3.689336162 -20.05694409
35.28671852 7.388193887 11.08780034 -1.882037195 32.36344521
35.37931111 8.424397777 11.57166807 7.107808696 1.723345683
35.4719037 9.558154575 12.93225367 7.586515831 -37.00550628
35.5644963 10.79125145 13.3853763 -2.692791469 0.03550648156
35.65708889 12.00757999 12.88762444 -2.682928558 32.37141523
35.74968148 13.20357423 13.22338395 6.309131228 -3.726283505
35.84227407 14.47909422 14.29590096 5.274052477 -33.69818989
35.93486667 15.82125454 14.40585435 -4.086555826 3.858529155
36.02745926 17.12315734 13.74832676 -3.014742172 23.79863064
36.12005185 18.38919613 13.80214587 3.595988562 7.016595363
36.21264444 19.7035724 14.64853767 5.545042829 -19.05335255
36.30523704 21.09233312 15.18534209 0.2524448975 -17.86328513
36.39782963 22.48636717 14.77264451 -4.709578749 12.47531557
36.49042222 23.82373089 14.22136747 -1.244213313 17.46991668
36.58301481 25.14372523 14.44028673 3.608541321 -6.306946543
36.67560741 26.50671958 14.94631941 1.856611726 -6.871653283
36.7682 27.90110056 15.11339635 -0.05218085298 -8.117517769
36.86079259 29.2935978 14.89494933 -2.3070469 0.9421177411
36.95338519 30.65372845 14.49194985 -2.045347527 -0.64438785
37.04597778 31.97752856 14.09660803 -2.224344152 -1.157585254
37.13857037 33.26278095 13.65491916 -2.545895612 12.72849447
37.23116296 34.51540265 13.51083598 0.9897972959 1.484741499
37.32375556 35.77607054 13.73231957 1.40222549 0.01634356657
37.41634815 37.05961641 13.99241132 1.40676537 -3.670354204
37.50894074 38.36435715 14.15852131 0.3872225353 -16.33010908
37.60153333 39.66568779 13.81021609 -4.148918875 -13.03849179
37.69412593 40.89849083 12.70654563 -7.77072215 17.01578767
37.78671852 42.0219091 11.70517187 -3.044114464 14.3230543
37.87931111 43.09099303 11.50983828 0.9345117306 3.936024886
37.9719037 44.16785528 11.78413122 2.027851977 8.223053424
38.0644963 45.28289182 12.37115765 4.312033483 -17.22834538
38.15708889 46.45166171 12.72656649 -0.4736180112 -17.22834538
38.24968148 47.61231057 0 0 0
---------------------------------------------
So, is the error (maximum number of table atoms exceeded) related to the .pot file? And how is the .pot file generated?
Thanks a lot for your replying


Edited by tyrion_jj (03/29/19 02:49 AM)

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#37449 - 03/29/19 04:10 AM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rongzhenliao]
tyrion_jj Offline
Forum Member

Registered: 01/08/19
Posts: 19
Hi everyone,
This is my input files and script. Thanks for helping me.


Attachments
charmm.zip (72 downloads)
Description: Hi everyone, This is my input files and script. Thanks for helping me.



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#37450 - 03/29/19 04:15 AM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rmv]
tyrion_jj Offline
Forum Member

Registered: 01/08/19
Posts: 19
Hi Rick,
I want to know whether the error could influence my simulation result? I found that the simulation could be still in progress although the error exist. Thanks a lot!

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#37451 - 03/29/19 10:57 AM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rongzhenliao]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8336
Loc: 39 03 48 N, 77 06 54 W
I have no experience with SBOUND, so there's not much I can add.
_________________________
Rick Venable
computational chemist


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#37452 - 03/29/19 06:37 PM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: rongzhenliao]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4724
Loc: ~ 59N, 15E
Yes. The simulation will not be what you think. You have forced CHARMM to neglect a serious error (bomlev -2). NEVER RUN A CALCULATTION THAT REQUIRES YOU TO CHANGE THE DEFAULT BOMLEV (unless you really know what your are doing) At the very least some atoms will NOT be subject to the sbound force.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37453 - 03/29/19 06:51 PM Re: CHARMM 39b2: maximum number of table atoms exceeded [Re: tyrion_jj]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4724
Loc: ~ 59N, 15E
It is related to the number of atoms that may be subjected to the sbound force. How many water oxygens do you have within the SBOUND sphere? The default size of the SBOUND table should be OK for a ~40A radius sphere.

For help with input files: Always submit a minimal file (the shortest possible!!!) that leads to the problem you observe.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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