AMBER Archive (2009)

Subject: Re: [AMBER] errors on REMD

From: z g (zgong.hust_at_gmail.com)
Date: Tue Jan 20 2009 - 07:39:12 CST

I'm using the "amber9" for REMD
Thank you very much!

2009/1/20 Carlos Simmerling <carlos.simmerling_at_gmail.com>

> your input looks like it may have some problems, but I cannot know
> unless you tell me which amber version you are using.
>
> On Mon, Jan 19, 2009 at 9:41 PM, z g <zgong.hust_at_gmail.com> wrote:
> > 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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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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