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Joined: Apr 2022
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Can someone explain what this means?
I'm trying to run this simulation but I keep getting this error after running the following script right after "@fbeta":


if @?gpu eq 1 then
set fbeta =
set omm = omm gamma 5
else
set fbeta = scalar fbeta set 5 select .not. hydrogen end
set omm =
endif

read rtf card name top_all36_prot.rtf
read param card flex name par_all36m_prot.prm

if @?built ne 0 goto built

open unit 10 read card name "1ic2.chainA.pdb"
read SEGI proa build setup first ace last ct3 unit 10

open unit 10 read card name "1ic2.chainB.pdb"
read SEGI prob build setup first ace last ct3 unit 10

open unit 10 read card name "antiTM.pdb"
read SEGI proc build setup first ace last ct3 unit 10


print coor select .not. ( initialized .or. hydrogen ) end

ic param
ic build

print coor select .not. initialized end

coor copy compare
cons harm force 50 select .not. hydrogen end
mini sd nstep 1000
mini abnr nstep 500
cons harm clear
coor orie rms select .not. hydrogen end

cons harm clear
coor orie rms select .not. hydrogen end

write coor pdb name 1ic2.chainAB.antiTM.min.pdb
write psf card name 1ic2.chainAB.antiTM.min.psf

delete atom select all end

label built


read psf card name 1ic2.chainAB.antiTM.min.psf
read coor pdb name 1ic2.chainAB.antiTM.min.pdb resi

! Now set-up and carry-out Langevin dynamics using the
! GBMV implicit solvent model (either on GPU or not)

! Setup the nonbonded cutoffs for GBMV energy calculations
set ctofnb = 38
set ctonnb = @ctofnb
calc cutnb = @ctofnb + 4
set cutim = @cutnb
NBOND atom switch cdie vdw vswitch - ! imall - !bycb
ctonnb @ctonnb ctofnb @ctofnb cutnb @cutnb cutim @cutim

prnlev 0
scalar wmain = radii
stream radii_c36gbmvop.str ! optimized input radii

prnlev 5
GBMV BETA -12 P3 0.65 WATR 1.4 SHIFT -0.102 SLOPE 0.9085 P6 8 SA 0.005 -
WTYP 2 NPHI 38 CUTNUM 100 KAPPA 0 weight

shake bonh tol 1e-7 param

open unit 13 write unform name 1ic2.chainAB.antiTM.min.dcd
open unit 14 write form name 1ic2.chainAB.antiTM.min.res

set temp = 298
set nstep = 50000000
set exch = 10000
calc nprt = 2 * @exch

@fbeta

dyna leap lang start timestep 0.002 nstep @nstep finalt @temp -
inbfreq -1 imgfreq -1 bygr -
iasors 1 iasvel 1 -
ntrfrq @nstep -
nprint @exch iprfrq @nprt nsavc @exch nsavv 0 iunvel -1 -
tstru @temp firstt @temp -
tbath @temp rbuf 0 ilbfreq 0 -
echeck -1 -
iunrea 0 isvfrq @nprt iunwri 14 iuncrd 13 kunit -1 -
@omm


stop

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too complicated. Please post a very short example file which exhibits the problem you encounter, without CHARMM variables. Also post the output.
I am not sure about READ SEGI; this is not the usual way to setup a system in CHARMM.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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I'm not quite sure how to simplify but here is the output file:

Attached Images
input.txt (71.8 KB, 47 downloads)
SHA1: abee45b4371d9fe8e7285ca759e3057ac5c5e4e3
Joined: Sep 2003
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1/ The error occurs when you run dynamics, not after @fbeta
2/ There is something wrong with your system, the energy is extremely high.
3/ The error message indicates that your system too large, or needs an internal array to be larger than its current dimension.
Fix point 2 and try again.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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I see! Thank you very much!


Moderated by  BRBrooks, lennart, rmv 

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