Re: [AMBER] neb/amber 10

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Fri, 26 Mar 2010 11:13:14 -0400

after looking at this again, the correct workaround to skip the LES
adjustment should be

      if( ipimd.eq.0 .and. ineb.eq.0) then

make sure not to use this code in general, though, it's just for the case
discussed below. Amber11 will have a much better treatment.

On Sat, Mar 13, 2010 at 8:21 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> I checked and it's safe to turn off the nlesadj check in rdparm.f is you're
> using LES only for NEB.
>
> just to make it clear, though, this is only for NEB using GB with the LES
> method.
> let me know if this is at all unclear.
>
> make this change in rdparm.f (change the first line with ipimd):
>
> change
> if( ipimd.eq.0 ) then
> ! pimd are not going to use nb_adjust_les, so we do not need to
> generate
> ! les adjust list
> !
> do 6500 k=1,natom
>
> to
> if( ipimd.eq.0 .or.ineb.eq.1) then
> ! pimd are not going to use nb_adjust_les, so we do not need to
> generate
> ! les adjust list
> !
> do 6500 k=1,natom
>
>
>
>
> On Wed, Mar 3, 2010 at 2:12 PM, Guillermina Estiu <gestiu.nd.edu> wrote:
>
>> Hi,
>> I am trying to find the path between two conformations of a same
>> molecule (~5000 atoms) using NEB in AMBER10.
>> I've prepared the .top and .crd files using addles, following the
>> instructions given in the manual. It worked after increasing maxdih, for a
>> maximum number of 14 copies.
>>
>> Again, according to the manual, I used the input file in the tutorial
>> (Ross Walkerís) to heat up the system.
>>
>> &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'
>> /
>>
>> Running the sander.LES.MPI executable, with my system size, results in the
>> error:
>>
>> LES parameters were found
>> EXCEEDED MAXLESADJ!
>>
>> I found the MAXLESADJ parameter to be set to a value of 3000000. I am not
>> sure if I just have to increase the value. Iíve found some discussion on the
>> list but not clear answer for this.
>>
>> I have tried the test case of the tutorial, addles works perfectly but
>> sander.LES
>> crash with an error: Floating point exception signaled at 7170b9: integer
>> divide by zero.
>>
>> There seems to be two different issues here, one related to the size of
>> the system. I have seen several posts like this one in the list but not the
>> solution. Any help on this?
>>
>> Thanks,
>> Guille
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Fri Mar 26 2010 - 08:30:02 PDT
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