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#22724 - 11/05/09 12:50 AM qchem/charmm test (alanine_qchem.inp)
Cass Forum Member Registered: 11/13/04 Posts: 13	I'm just compiled the qchem-charmm interface and ran my first QM/MM script provided with charmm package in the test sub-directory - alanine_qchem.inp. There are a couple of things I don't fully understand. 1)The analytic and finite difference of the first derivative vary considerably for the QM/MM calculation. 2) When I run it with all atoms selected for the QM calculation the forces are very different as compared to when I select all atoms for the MM calculation. Here is part of the input and output file below. Any insight into this would be greatly appreciated. Quote: .............. read sequ ala 1 gene mpep setup ........ mini abnr nstep 1000 nprint 1000 addl qqh mpep 1 c mpep 1 ca !---------- Needed to define Q-Chem env. vars. ---------- envi qchemcnt "../data/qchem.inp" envi qcheminp "q1.inp" envi qchemexe "qchem" envi qchemout "qchem.out" !-------------------------------------------------------- define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - .or. atom mpep 1 ot2 end qchem remove sele qm end ........... energy ........... scal xcomp = x scal ycomp = y scal zcomp = z scal x = dx scal y = dy scal z = dz open write card unit 1 name @9/test2.frc write coor card unit 1 * forces after qchem * ! restore forces scal x = xcomp scal y = ycomp scal z = zcomp test first tol 0.0 step 0.0005 stop When it gets to >test first tol 0.0 step 0.0005 I get the following output. Quote: CHARMM> test first tol 0.0 step 0.0005 TESTFD: Parameters: STEP= 0.00050 MASSweighting= 0 TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( MPEP 1 ALA N ) -25.60395646 -2.81441381 -22.78954265 1 Y ( MPEP 1 ALA N ) -61.48556283 -3.91825670 -57.56730613 1 Z ( MPEP 1 ALA N ) 7.71936465 0.58564852 7.13371613 2 X ( MPEP 1 ALA HT1 ) -15.13274527 -0.64366373 -14.48908153 2 Y ( MPEP 1 ALA HT1 ) 3.52494396 0.30699349 3.21795047 2 Z ( MPEP 1 ALA HT1 ) 1.01922610 -0.52711260 1.54633870 3 X ( MPEP 1 ALA HT2 ) 27.04379801 -0.44955000 27.49334801 3 Y ( MPEP 1 ALA HT2 ) 13.22514800 1.37404358 11.85110442 3 Z ( MPEP 1 ALA HT2 ) -2.25123940 -0.15046120 -2.10077820 4 X ( MPEP 1 ALA HT3 ) -11.81808050 -0.61318582 -11.20489467 4 Y ( MPEP 1 ALA HT3 ) -45.62655549 0.45260243 -46.07915792 4 Z ( MPEP 1 ALA HT3 ) 4.48234812 0.41055298 4.07179514 5 X ( MPEP 1 ALA CA ) 0.02135112 0.02130879 0.00004233 5 Y ( MPEP 1 ALA CA ) -0.11916342 -0.11913049 -0.00003293 5 Z ( MPEP 1 ALA CA ) -0.75963003 -0.75962092 -0.00000911 6 X ( MPEP 1 ALA HA ) 0.89230779 0.55309189 0.33921590 6 Y ( MPEP 1 ALA HA ) 4.84779599 2.03572382 2.81207217 6 Z ( MPEP 1 ALA HA ) -2.63247901 -0.83904761 -1.79343139 7 X ( MPEP 1 ALA CB ) -1.25577086 -0.96197687 -0.29379399 7 Y ( MPEP 1 ALA CB ) -11.71623815 -4.20655012 -7.50968803 7 Z ( MPEP 1 ALA CB ) -3.55996716 -0.50714018 -3.05282697 8 X ( MPEP 1 ALA HB1 ) 0.27721486 0.11549017 0.16172469 8 Y ( MPEP 1 ALA HB1 ) 1.64560931 0.01947563 1.62613368 8 Z ( MPEP 1 ALA HB1 ) 0.25701250 -0.09946911 0.35648161 9 X ( MPEP 1 ALA HB2 ) 0.44623685 0.20086324 0.24537361 9 Y ( MPEP 1 ALA HB2 ) 1.98284551 0.25557868 1.72726683 9 Z ( MPEP 1 ALA HB2 ) 1.19780304 -0.28476115 1.48256418 10 X ( MPEP 1 ALA HB3 ) -0.16279571 0.34492357 -0.50771928 10 Y ( MPEP 1 ALA HB3 ) 2.76551953 0.34327316 2.42224637 10 Z ( MPEP 1 ALA HB3 ) 0.82897966 -0.14127715 0.97025681 11 X ( MPEP 1 ALA C ) -1.65613199 -55.17516611 53.51903412 11 Y ( MPEP 1 ALA C ) 9.16764803 -152.94164515 162.10929318 11 Z ( MPEP 1 ALA C ) 3.23332492 22.48995446 -19.25662953 12 X ( MPEP 1 ALA OT1 ) -12.95704517 46.24019520 -59.19724036 12 Y ( MPEP 1 ALA OT1 ) -26.36381216 -15.76495801 -10.59885415 12 Z ( MPEP 1 ALA OT1 ) 3.90709232 3.78861713 0.11847519 13 X ( MPEP 1 ALA OT2 ) -0.05299862 -35.97013504 35.91713642 13 Y ( MPEP 1 ALA OT2 ) -1.18242367 14.58055076 -15.76297443 13 Z ( MPEP 1 ALA OT2 ) 0.42239897 -1.55231109 1.97471006 14 X ( MPEP 1 ALA QQH1) 0.00000000 49.15219163 -49.15219163 14 Y ( MPEP 1 ALA QQH1) 0.00000000 157.58225640 -157.58225640 14 Z ( MPEP 1 ALA QQH1) 0.00000000 -22.41357257 22.41357257 TESTFD: A total of 0 elements were within the tolerance Thanks. Edited by Cass (11/06/09 05:23 PM)
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#23142 - 01/08/10 07:21 AM Re: qchem/charmm test (alanine_qchem.inp) [Re: Cass]
laura Forum Member Registered: 01/23/04 Posts: 19 Loc: Spain	Hi, I am also trying the qchem/charmm interface and it run ok. (serial version so far) Here you have the output of the gradient test (run as it is in the testcase): You are running Q-Chem version: 3.2.0.2 TESTFD: Parameters: STEP= 0.00050 MASSweighting= 0 TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( MPEP 1 ALA N ) -2.81443362 -2.81439687 -0.00003675 1 Y ( MPEP 1 ALA N ) -3.91834179 -3.91824162 -0.00010017 1 Z ( MPEP 1 ALA N ) 0.58571248 0.58570391 0.00000858 2 X ( MPEP 1 ALA HT1 ) -0.64367455 -0.64366942 -0.00000513 2 Y ( MPEP 1 ALA HT1 ) 0.30697963 0.30701928 -0.00003964 2 Z ( MPEP 1 ALA HT1 ) -0.52714858 -0.52708585 -0.00006273 3 X ( MPEP 1 ALA HT2 ) -0.44958757 -0.44957441 -0.00001316 3 Y ( MPEP 1 ALA HT2 ) 1.37402235 1.37408360 -0.00006125 3 Z ( MPEP 1 ALA HT2 ) -0.15045698 -0.15048227 0.00002529 4 X ( MPEP 1 ALA HT3 ) -0.61319618 -0.61313523 -0.00006096 4 Y ( MPEP 1 ALA HT3 ) 0.45256726 0.45250000 0.00006726 4 Z ( MPEP 1 ALA HT3 ) 0.41056236 0.41052757 0.00003479 5 X ( MPEP 1 ALA CA ) 0.02135058 0.02130827 0.00004231 5 Y ( MPEP 1 ALA CA ) -0.11917426 -0.11914133 -0.00003293 5 Z ( MPEP 1 ALA CA ) -0.75963198 -0.75962287 -0.00000911 6 X ( MPEP 1 ALA HA ) 0.55309302 0.55308448 0.00000854 6 Y ( MPEP 1 ALA HA ) 2.03572894 2.03575168 -0.00002273 6 Z ( MPEP 1 ALA HA ) -0.83902957 -0.83905268 0.00002311 7 X ( MPEP 1 ALA CB ) -0.96195231 -0.96196396 0.00001165 7 Y ( MPEP 1 ALA CB ) -4.20652871 -4.20653864 0.00000993 7 Z ( MPEP 1 ALA CB ) -0.50714547 -0.50710161 -0.00004386 8 X ( MPEP 1 ALA HB1 ) 0.11550075 0.11549117 0.00000958 8 Y ( MPEP 1 ALA HB1 ) 0.01953798 0.01947848 0.00005950 8 Z ( MPEP 1 ALA HB1 ) -0.09948759 -0.09948901 0.00000142 9 X ( MPEP 1 ALA HB2 ) 0.20088025 0.20085783 0.00002242 9 Y ( MPEP 1 ALA HB2 ) 0.25558393 0.25565461 -0.00007068 9 Z ( MPEP 1 ALA HB2 ) -0.28475322 -0.28472613 -0.00002709 10 X ( MPEP 1 ALA HB3 ) 0.34490223 0.34492010 -0.00001787 10 Y ( MPEP 1 ALA HB3 ) 0.34331226 0.34328731 0.00002495 10 Z ( MPEP 1 ALA HB3 ) -0.14125222 -0.14125484 0.00000262 11 X ( MPEP 1 ALA C ) -55.17533512 -55.17498626 -0.00034886 11 Y ( MPEP 1 ALA C ) -152.94122165 -152.94141196 0.00019031 11 Z ( MPEP 1 ALA C ) 22.49211943 22.49209989 0.00001955 12 X ( MPEP 1 ALA OT1 ) 46.24005928 46.24023012 -0.00017084 12 Y ( MPEP 1 ALA OT1 ) -15.76465579 -15.76479361 0.00013782 12 Z ( MPEP 1 ALA OT1 ) 3.78878818 3.78873860 0.00004958 13 X ( MPEP 1 ALA OT2 ) -35.96960744 -35.97013329 0.00052585 13 Y ( MPEP 1 ALA OT2 ) 14.58046440 14.58049251 -0.00002812 13 Z ( MPEP 1 ALA OT2 ) -1.55249726 -1.55248634 -0.00001092 14 X ( MPEP 1 ALA QQH1) 49.15200247 49.15200337 -0.00000090 14 Y ( MPEP 1 ALA QQH1) 157.58172662 157.58206816 -0.00034154 14 Z ( MPEP 1 ALA QQH1) -22.41577972 -22.41570610 -0.00007362 TESTFD: A total of 0 elements were within the tolerance I am not sure to understand your second question. Laura
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#23148 - 01/08/10 03:16 PM Re: qchem/charmm test (alanine_qchem.inp) [Re: Cass]
Kenno Forum Member Registered: 12/19/05 Posts: 472 Loc: Baltimore, MD	Originally Posted By: Cass There are a couple of things I don't fully understand. 1)The analytic and finite difference first derivatives vary considerably for the QM/MM calculation. 2) When I run it with all atoms selected for the QM calculation the forces are very different as compared to when I select all atoms for the MM calculation. I'm probably not understanding the question correctly either, but aren't both of these observations expected behaviour?
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