AMBER Archive (2008)

Subject: Re: AMBER: Problem running NEB in AMBER10

From: Chris C. (chris.bc57_at_gmail.com)
Date: Wed Dec 03 2008 - 12:29:48 CST

Hi Ross,
My addles input seems OK to me...
file rprm name=(BCDOP.top) read
file rcrd name=(BCDOP.crd) pack=2 read
file wprm name=(BCDOP_NEB.top) wovr
file wcrd name=(BCDOP_NEB.crd) wovr
action
~ use original mass
omass
pimd
~ make 20 copies of atom 1 to 244 (the whole system)
space numc=20 pick #prt 1 244 done
*EOD

I sent you last week my top and crd on your personal email adress.
Did you receive them ?
Regards,
Chris

2008/11/26 Ross Walker <ross_at_rosswalker.co.uk>:
> 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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of Chris C.
>> Sent: Wednesday, November 26, 2008 10:38 AM
>> To: amber_at_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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