Hello,
This is the input file for equilibration stage of remd.
----------------------------------------
Equilibration
&cntrl
irest=0, ntx=1,
nstlim=100000, dt=0.0005,
irest=0, ntt=3, gamma_ln=1.0,
temp0=XXXXX, ig=RANDOM_NUMBER,
ntc=2, ntf=2, nscm=1000,
ntb=0, igb=5,
cut=999.0, rgbmax=999.0,
ntpr=500, ntwx=500, ntwr=100000,
nmropt=1,
/
&wt TYPE='END'
/
DISANG=heh03.dat
--------------------------------------
And I attached all prmtop, inpcrd, rst and input mdin files with zip.
You can execute it by the following command.
sander.MPI -ng 12 -groupfile equilibrate.groupfile
Thank you.
Bongkeun Kim
Quoting case <case.biomaps.rutgers.edu>:
> On Wed, Feb 16, 2011, Bongkeun Kim wrote:
>
>> I did the same thing with ff99SB force field and I got the same error.
>
>> I generated input files from tleap by using the following sequence.
>> sequence {NGLU GLU ARG VAL GLN ASP ASN ILE VAL ASN ARG ILE SER ASP ARG CLEU
>> }
>> It worked well with the single MD with pmemd.cuda.
>> sander.mpi with REMD only has this error and adding ACE cap onto the
>> first GLU makes me avoid this error.
>
> Can you post what your groupfile and input files look like? It would help
> also if you posted the prmtops and input coordinate files. The more work it
> is for someone to reproduce the problem, the less likely they are to examine
> it. This is an unusual problem, but there might even be simple things wrong
> with the REMD inputs that are hard to imagine with the current (lack of)
> information, but which might become obvious when someone saw your
> actual input
> files.
>
> And, of course, you may be able to solve this problem yourself:
> start with the
> working REMD examples in the test cases (e.g. $AMBERHOME/test/rem_gb_2rep,
> etc.) and try to slowly morph them into your system. For example, use the
> same groupfile and input files as in the test case, but substitute in your
> prmtop and incprd files. This is all a part of narrowing down the problem.
>
> ....dac
>
>
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Received on Thu Feb 17 2011 - 10:30:04 PST
