AMBER Archive (2009)

Subject: Re: [AMBER] errors on REMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jan 26 2009 - 11:38:39 CST

look at the inpcrd files you use for remd- are the coordinate values
large? I think you'll need to do some troubleshooting yourself to see
exactly when these numbers get big.

On Thu, Jan 22, 2009 at 8:02 PM, z g <zgong.hust_at_gmail.com> wrote:
> Dear sir :
> I have followed your advise to change my mdin files like this
> Equilibration
> &cntrl
> irest=1, ntx=5,
> nstlim=10000, dt=0.001,
> ntt=3, gamma_ln=1.0,
> temp0=XXXXX, ig=RANDOM_NUMBER,
> ntc=2, ntf=2, nscm=1000,
> ntb=0, igb=1,
> cut=999.0, rgbmax=999.0,
> ntpr=1000, ntwx=1000, ntwr=100000,
> nmropt=1,
> numexchg=1000,
> /
> &wt TYPE='END'
> /
> However, the same erros happened again
>
> input conversion error, unit 9, file /export/home/md/remd.rst.007
>
> the remd.rst.007 file like
>
>
> 389 0.1360000E+04 0.3756000E+03
> -67.9667402 143.5693955 135.3920753 26.3374926 259.7714224-374.0863183
> 27.2250652 258.8290660-374.5986003-138.7437384-753.0304527 -24.6733927
> 578.0399447 544.7979446-203.7098287 27.3056520 258.7732931-376.0732231
> -673.6576239 334.1924531-697.6538998 28.2680961 259.7702090-376.4543691
> 29.0208772 259.2781126-377.5736472 42.6589530 585.2045901-745.6005556
> 30.4860660 258.9320589-377.4628697 31.2380916 258.3566393-378.4070212
> -302.2943711 -56.2521559************ 32.5331551 258.2713939-378.2040061
>
> before I do the remd, I have I have run 1ns simulations with each replica to
> equilibrate them to their individual temperatures
> my amber version is amber9
> what should I do ?
>
> Thank you very much!
>
>
>
> 2009/1/20 Carlos Simmerling <carlos.simmerling_at_gmail.com>
>
>> I don't think your main problem is unique to remd. however, your
>> inputs will probably not work properly for remd. make sure to read the
>> manual carefully, especially the section "cautions when using replica
>> exchange".
>>
>> one of your problems is specifically discussed there:
>> irest should be 1, not 0. ntx should be 5. you almost certainly don't
>> want to reassign velocities each exchange. this will very likely
>> interfere with correct equilibration and probably cause exchanges to
>> be incorrect.
>> Amber10 has much improved input checks and other improvements for remd.
>>
>> regarding your problem with coordinates, this is not REMD related but
>> indicates that your system has diffused so far from the origin that
>> the coordinates don't fit in the formatted file. I have never had this
>> happen with ntt=3, though I guess it is possible. using nscm>0 will
>> resolve it, though should be needed for ntt=3. did you run with ntt=0
>> or 1 at some point? is there a reason the system would be so far from
>> the origin?
>>
>>
>>
>> On Tue, Jan 20, 2009 at 8:39 AM, z g <zgong.hust_at_gmail.com> wrote:
>> > 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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>> >> >
>> >>
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