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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 Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
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: 4741
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: 4741
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 Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
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 (97 downloads)
Description: Hi everyone, This is my input files and script. Thanks for helping me.



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