After an equilibration run at 305 K I attempted to start the production
run but
I got this error message:
EWALD BOMB in subroutine ewald_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander.
Here are the input files I used for my calculation:
=================================================================
cat <<eof > mdin
MD in formaldehyde box ntp,warm to 305K quickly, tight pressure coupling
for fast density adj.
&cntrl
imin=0,
igb = 0, ntpr = 500, ntwx = 500, ntwe=500,
vlimit=10, nsnb = 20,
cut = 12.0, ntp=1, taup=0.01, ntr=1,
tempi = 305.0, temp0 = 305.0, ntt = 1,
nstlim = 20000, dt = 0.001,
ntx=7, irest=1, ntb=2, ntc=2, ntf=2,
&end
Restrain heavy atoms
100.0
FIND
* C * *
* CA * *
* CC * *
* CR * *
* CT * *
* CV * *
* OH * *
* O2 * *
SEARCH
RES 23 23 46 46 115 115 92 92 69 69 230 230
RES 207 207 184 184 322 322 299 299 276 276 161 161
RES 138 138 253 253 345 345
RES 1 1 24 24 47 47 116 116 93 93 70 70 231 231
RES 208 208 185 185 323 323 300 300 277 277 162 162
RES 139 139 254 254
END
Restrain heavy atoms II
100.0
FIND
* O * *
* NA * *
* N * *
* N2 * *
* NB * *
* N3 * *
* S * *
SEARCH
RES 23 23 46 46 115 115 92 92 69 69 230 230
RES 207 207 184 184 322 322 299 299 276 276 161 161
RES 138 138 253 253 345 345
RES 1 1 24 24 47 47 116 116 93 93 70 70 231 231
RES 208 208 185 185 323 323 300 300 277 277 162 162
RES 139 139 254 254
END
END
eof
sander -O -i mdin \
-c col23formWATmd1.rst -ref col23formWAT.rst -p col23formWAT.top -o
col23formWAT.md2.out -x col23formWATmd2.traj -r col23formWATmd2.rst
==============================================================================================
cat <<eof > mdin
MD in formaldehyde box ntp, continue at 305K with relaxed pressure coupling
&cntrl
imin=0,t=0.0,
igb = 0, ntpr = 1000, ntwx = 1000, ntwe=1000,
vlimit=10, nsnb = 20, ntr=1,
cut = 12.0, ntp=1, taup=1.0,
tempi = 305.0, temp0 = 305.0, ntt = 1,
nstlim = 1100000, dt = 0.001,
ntx=7, irest=1, ntb=2, ntc=2, ntf=2,
&end
Restrain heavy atoms
100.0
FIND
* C * *
* CA * *
* CC * *
* CR * *
* CT * *
* CV * *
* OH * *
* O2 * *
SEARCH
RES 23 23 46 46 115 115 92 92 69 69 230 230
RES 207 207 184 184 322 322 299 299 276 276 161 161
RES 138 138 253 253 345 345
RES 1 1 24 24 47 47 116 116 93 93 70 70 231 231
RES 208 208 185 185 323 323 300 300 277 277 162 162
RES 139 139 254 254
END
Restrain heavy atoms II
100.0
FIND
* O * *
* NA * *
* N * *
* N2 * *
* NB * *
* N3 * *
* S * *
SEARCH
RES 23 23 46 46 115 115 92 92 69 69 230 230
RES 207 207 184 184 322 322 299 299 276 276 161 161
RES 138 138 253 253 345 345
RES 1 1 24 24 47 47 116 116 93 93 70 70 231 231
RES 208 208 185 185 323 323 300 300 277 277 162 162
RES 139 139 254 254
END
END
eof
sander -O -i mdin \
-c col23formWATmd2.rst -ref col23formWAT.rst -p col23formWAT.top -o
col23formWAT.mdRUN.out -x col23formWATmd3.traj -r col23formWATmdRUN.rst
=====================================================================================
I would be deeply grateful for any advice you can give me.
Susanna Monti
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
Dr. Susanna Monti
IPCF-CNR
http://www.ipcf.cnr.it
Area della Ricerca di Pisa
Via G. Moruzzi 1
56124 PISA (Italy)
Voice +39-050-3152520 FAX +39-050-3152442
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Received on Wed Jul 30 2003 - 14:53:00 PDT
