Dear sir :
I would like to use amber9 to perform REMD on RNA molecule. However,
I met some errors during the simulation.
At first, Before starting the REMD simulations we have run 1ns simulations
with each replica to equilibrate them to their individual temperatures. I
have use 8 replicas with temperatures( 270,285,300,315,330,345,370,380). The
RNA molecule contains 389 atoms.
My mdin files for REMD like
RNA REMD
&cntrl
irest=0, ntx=1,
nstlim=10000, dt=0.001,
irest=0, ntt=3, gamma_ln=1.0,
temp0=287.3, ig=7988,
ntc=2, ntf=2,
ntb=0, igb=1,
cut=999.0, rgbmax=999.0,
ntpr=1000, ntwx=1000, ntwr=100000,
nmropt=1,
numexchg=1000,
/
&wt TYPE='END'
/
At first, the program run correctly, while after 1 hour, some errors happen
forrtl: severe (64): input conversion error, unit 9, file
/export/home/1zih_remd//remd.rst.007
I have watched the remd.rst.007, and find the numbers are very large
389 0.1300000E+04 0.3592000E+03
-105.8953861 748.7806467-468.5337764-100.7161016 24.3022386-170.1731608
-101.4099610 24.3477791-168.9152646-471.2815199 -14.2248508-271.6494052
-49.2667843 548.1655243 82.0420727-101.1563083 23.2039701-167.8895453
-213.6132285 301.0739486 451.6375036-102.1736480 22.2559916-168.1535552
-101.4738436 20.9869045-168.1231668 -75.7654453-315.9162929 590.7650174
-102.0262742 20.0482355-169.1328678-101.5804244 19.7278654-170.3871519
534.9756401 508.7310783-616.9927623-102.2027898 18.7924921-171.0093015
-103.0636418 18.3286643-169.9952243-104.0138694 17.1960597-170.0369936
-104.3907387 16.3896575-170.8753573-104.6018766 16.9349549-168.7753226
-503.6963882-583.9394758 -15.3460633-104.5414249 17.8285116-167.7480043
-105.1545082 17.4537929-166.6067724-535.9608133-746.2963594 -95.6632087
171.1120712 444.0063185 577.8922425-103.6933133 18.8393584-167.6861132
-103.0122636 19.0754130-168.8968330 -99.7914615 22.5807460-167.9552119
417.3237163 541.2504776-584.2170254-100.0500924 21.2862850-168.6877856
-252.8170614 80.7117256************ -99.0037521 20.3504289-168.5717094
443.9874455 196.9228391-437.3244152 -99.3986068 22.4688989-166.6403937
What should I do to fix this problem?
Thank you !
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Received on Wed Jan 21 2009 - 01:15:53 PST
