[gmx-users] Entropy from NMA

[Ran Friedman]

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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