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.gmail.com> wrote:
> I'm using the "amber9" for REMD
> Thank you very much!
>
> 2009/1/20 Carlos Simmerling <carlos.simmerling.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.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 !
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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Received on Wed Jan 21 2009 - 01:21:45 PST
