Hi Chris,
How did you create your prmtop and inpcrd files?
The key point is how you run addles to build the combined prmtop:
file rprm name=(str1.prmtop) read
file rcrd name=(str1.inpcrd) pack=2 read
file wprm name=(neb.prmtop) wovr
file wcrd name=(neb.inpcrd) wovr
action
~ use original mass
omas
pimd
~ make 30 copies of atom 1 to 22 (the whole system)
space numc=30 pick #prt 1 22 done
*EOD
The key is that the 1 22 must be adjusted to match the number of atoms in
your prmtop files since NEB only works on the whole system. You also need to
make sure you include the omas and pimd flags.
Please check that you did this correctly and if you did then please send me
the original prmtop and inpcrd files, the ones you generated for each end
point so I can try them out.
All the best
Ross
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Chris C.
> Sent: Wednesday, November 26, 2008 10:38 AM
> To: amber.scripps.edu
> Subject: AMBER: Problem running NEB in AMBER10
>
> Hi,
> I am trying to find the path between two conformations of a same
> molecule (~250 atoms) using NEB (I'm using AMBER10 and have applied
> all the latest bugfixes).
> I've prepared the .top and .crd files using addles, following the
> instructions given in the manual. This step seems OK, as the files are
> created.
> Again, according to the manual, one shall run sander.MPI for NEB
> calculations.
> I'm using the input file provided by Ross Walker in his NEB tutorial, ie:
> NEB Initial MD
> &cntrl
> imin = 0, irest = 0,
> ntc=1, ntf=1,
> ntpr=50, ntwx=500,
> ntb = 0, cut = 999.0, rgbmax=999.0,
> igb = 1, saltcon=0.2,
> nstlim = 40000, nscm= 0,
> dt = 0.0005,
> ntt = 3, gamma_ln=1000.0,
> tempi=0, temp0=300,
> ineb = 1,skmin = 10,skmax = 10,
> nmropt=1
> /
> &wt type='TEMP0', istep1=0,istep2=35000,
> value1=0.0, value2=300.0
> /
> &wt type='END'
> /
>
> Sander crashes immediately and here is what I get
> | Flags: MPI
> *** THIS VERSION WILL NOT ACCEPT TOPOLOGY FILES
> THAT WERE CREATED BY ADDLES, WITH NPARM=1
> USE A VERSION COMPILED WITH -DLES
>
> I then tried to run my calculation with the sander.LES.MPI executable,
> and then another kind of error occurred
> LES parameters were found
> EXCEEDED MAXLESADJ!
>
> I found the MAXLESADJ parameter to be set to a value of 3000000.
> Is my system too big ? If so, should I increase this value and recompile ?
>
> Chris
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Received on Fri Dec 05 2008 - 17:54:17 PST
