[gmx-users] Entropy from NMA

[Ran Friedman]

p.s. How big is this negative value?

Ran Friedman wrote:
> Hi,
>
> Can you post the exact commands you used for EM and NMA?
>
> Ran
>
> nahren manuel wrote:
>> Dear Gromacs Users,
>>
>> I am trying to calculate Entropy from Normal Mode Analysis.
>> I minimized the structure to
>> 8.41750710592449e-09
>>
>> Then I calculated the normal mode (the mdp file is given below).
>>
>> But when i try to calculate the Eigenvalues, I get the following warning
>>
>>
>> One of the lowest 6 eigenvalues has a non-zero value.
>> This could mean that the reference structure was not
>> properly energy minimized.
>> Writing eigenvalues...
>>
>> I get only negative eigenvalues.
>>
>> Let me also add that I used the same mdp file for minimization
>> changing the integrator to steep, cg and finally to l-bfgs.
>>
>> Best,
>> nahren
>>
>> -----------------------
>> integrator    = nm     
>> constraints = none
>> define = -DFLEXIBLE
>> emtol        = 0.00000001    
>> emstep          = 0.00000001     
>> nsteps        = 50000       
>> nstlist        = 1      
>> ns_type        = grid    
>> rlist        = 1.5     
>> coulombtype    = shift     
>> rcoulomb-switch    = 1.0    
>> rvdw-switch        = 1.0      
>> vdwtype = shift
>> rcoulomb = 1.3
>> rvdw = 1.3
>>
>>
>
>
> -- 
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355559
> Email: r.friedman at bioc.uzh.ch
> Skype: ran.friedman
> ------------------------------------------------------
>   


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