[gmx-users] Normal Mode Analysis

[James Starlight]

I've used double precision. Today I'll copied output because it's done on
lab comp but from the output log I've found that minimization was not
completed ( e.g when I've calculate Normal Modes with that minimized
structure I've obtain message that my system was not minimized properly )

2011/10/26 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>> I've forced with the problem that I could not prorerly minimized my system
>> in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot
>> value lower than +3.00 with that parametries ( I've used KALP peptide as a
>> test input )
>>
>>
> The Epot value is less significant than Fmax (which is what is set in the
> .mdp file, anyway).  What Fmax do you achieve?  Real copied and pasted
> output would be useful.
>
>
>  ; Parameters describing what to do, when to stop and what to save
>> integrator    = steep       emtol        = 1      ; Stop minimization when
>> the maximum force < 1.0 kJ/mol/nm
>> emstep      = 0.01      ; Energy step size
>> nsteps        = 5000000          ; Maximum number of (minimization) steps
>> to perform
>>
>>
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist        = 1        ; Frequency to update the neighbor list and long
>> range forces
>> ns_type        = grid        ; Method to determine neighbor list (simple,
>> grid)
>> rlist        = 1.2        ; Cut-off for making neighbor list (short range
>> forces)
>> coulombtype    = Shift   rcoulomb        = 1.0
>> rcoulomb_switch    = 0.0
>> vdwtype         = Shift
>> rvdw        = 1.0
>> rvdw_switch     = 0.0
>> Than I've tried to futher minimized this structure via  l-bfgs algorithm
>> by
>>
>> integrator    = l-bfgs
>> dt                  =  0.01
>> emtol        = 0.001     ;
>> emstep      = 0.1      ; Energy step size
>> nsteps        = 50000000          ; Maximum number of (minimization) steps
>> to perform
>>
>> but Epot was still big.
>>
>> What I've done wrong ?
>>
>
> Are you using single- or double-precision?
>
> -Justin
>
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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