[gmx-users] Entropy from NMA

Wed Jul 28 12:48:12 CEST 2010

Dear Ran,

I ran the whole NMA again and I found where I go wrong. I hope it will help others as well.
(sorry for a big email)

In steps 1 & 2 (of minimization) I kept the C-alpha frozen.

1. doublegrompp -f em1.mdp -c r1dodecapdb.pdb -p r1top.top -o em1tpr.tpr
mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em1tpr

Steepest Descents converged to Fmax < 100 in 2569 steps
Potential Energy  = -6.21296128286120e+03
Maximum force     =  9.87358378592302e+01 on atom 701
Norm of force     =  1.04875323563923e+01

2. doublegrompp -f em2.mdp -c em1tpr.gro -p r1top.top -o em2tpr.tpr -t em1tpr.trr
mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em2tpr

Polak-Ribiere Conjugate Gradients converged to Fmax < 1 in 6596 steps
Potential Energy  = -7.56682084795001e+03
Maximum force     =  9.92719787231560e-01 on atom 1320
Norm of force     =  6.47772253797808e-02

3. doublegrompp -f em3.mdp -c em2tpr.gro -p r1top.top -o em3tpr.tpr -t em2tpr.trr
mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em3tpr

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 3018 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -8.49398064549505e+03
Maximum force     =  6.86336687926682e+01 on atom 935
Norm of force     =  7.15798864024085e+00

4. doublegrompp -f em4.mdp -c em3tpr.gro -p r1top.top -o em4tpr.tpr -t em3tpr.trr
mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em4tpr

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 0.01

writing lowest energy coordinates.

Polak-Ribiere Conjugate Gradients converged to machine precision in 21674 steps,
but did not reach the requested Fmax < 0.01.
Potential Energy  = -9.66058047638671e+03
Maximum force     =  1.49342602818840e+00 on atom 590
Norm of force     =  1.86576579430541e-01

5.doublegrompp -f em5.mdp -c em4tpr.gro -p r1top.top -o em5tpr.tpr -t em4tpr.trr
 ~/gmxdpr/bin/doublemdrun -v -deffnm em5tpr

Low-Memory BFGS Minimizer converged to machine precision in 10346 steps,
but did not reach the requested Fmax < 0.0001.
Potential Energy  = -9.66337416273684e+03
Maximum force     =  6.48625019025464e-04 on atom 581
Norm of force     =  6.35632681200205e-05

6.doublegrompp -f em6.mdp -c em5tpr.gro -p r1top.top -o em6tpr.tpr -t em5tpr.trr

Low-Memory BFGS Minimizer converged to machine precision in 3316 steps,
but did not reach the requested Fmax < 1e-08.
Potential Energy  = -9.66337416275038e+03
Maximum force     =  6.48788529801368e-05 on atom 8
Norm of force     =  6.56362137550289e-06

7. doublegrompp -f em7.mdp -c em6tpr.gro -p r1top.top -o em7tpr.tpr -t em6tpr.trr

Low-Memory BFGS Minimizer converged to machine precision in 7530 steps,
but did not reach the requested Fmax < 1e-08.
Potential Energy  = -9.66337416275071e+03
Maximum force     =  4.07762128402886e-07 on atom 10
Norm of force     =  5.79534451487287e-08

8. doublegrompp -f em8.mdp -c em7tpr.gro -p r1top.top -o em8tpr.tpr -t em7tpr.trr
Low-Memory BFGS Minimizer converged to Fmax < 1e-08 in 5840 steps
Potential Energy  = -9.66337416275070e+03
Maximum force     =  8.41750710592449e-09 on atom 521
Norm of force     =  1.28889193955553e-09

NMA

9. doublegrompp -f nma.mdp -t em8tpr.trr -c em8tpr.gro -p r1top.top -o nmatpr.tpr
~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr

(a sinlge processor)
 ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr
it created only one nmatpr.mtx
Maximum force: 8.41751e-09
Finished step 1400 out of 1400

It creates the output nmatpr.mtx nmatpr.edr etc....

Now I delete all nma files
rm nmatpr.*

(4 processor)
mpirun -np 4 ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr
Maximum force: 8.41768e-09
Maximum force: 8.41768e-09
Maximum force: 8.41768e-09
Maximum force: 8.41768e-09
Finished step 1399 out of 1400

Writing Hessian...

Writing Hessian...
Finished step 1400 out of 1400

Writing Hessian...

Back Off! I just backed up nmatpr.mtx to ./#nmatpr.mtx.2#

It gives me negative eigenvalues.

One would expect it should not create nmatpr.mtx.1 nmatpr.mtc.2 etc...since these files have been removed. Because it created multiple nmatpr.mtx file and backup one over another

I am not sure If the problem occurs with my system , but other MPIRUN (with mdrun) do not create such backup.

Best,
nahren

--- On Wed, 7/28/10, Ran Friedman <r.friedman at bioc.uzh.ch> wrote:

From: Ran Friedman <r.friedman at bioc.uzh.ch>
Subject: Re: [gmx-users] Entropy from NMA
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wednesday, July 28, 2010, 3:10 PM

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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