AMBER Archive (2004)

Subject: AMBER: vdw energy in minimization

From: anshul_at_imtech.res.in
Date: Mon Jul 19 2004 - 10:11:17 CDT

Hi all,
I am trying to run dynamics of a small decapeptide using explicit solvent
in amber 7. For this I solvated the system in wtbox as follows:

> loadpdb ala_an.pdb
Loading PDB file: ./ala_an.pdb
  total atoms in file: 112
> x=loadpdb ala_an.pdb
Loading PDB file: ./ala_an.pdb
  total atoms in file: 112
> solvatebox x WATBOX216 8 2
  Solute vdw bounding box: 18.845 16.817 12.703
  Total bounding box for atom centers: 34.845 32.817 28.703
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 37.435 35.779 31.349 angstroms.
  Volume: 41989.553 A^3
  Total mass 13845.496 amu, Density 0.548 g/cc
  Added 725 residues

After this I minimized the solvent by restraining the peptide unit. Input
for the same is:

&cntrl
   imin=1,
   maxcyc=15000, ncyc=4000, drms=0.001,
   ntb=1, ntr=1,
   cut=10,
   ntpr=50,
 &end Input for restraints (1-12) 10 RES 1 12 END
END

During minimization I observed that the total energy of the system
decreased gradually (became more and more negative) but the vdw energy
kept on increasing till the end. this thing was followed in the next step
of minimization of the whole system without any restraints. The output
file is attached with the mail for reference.

Can anyone help me with this and tell what is wrong with the system. I
visualized the system with the water box and it looked ok to me.

Next when ZI ran constant volume dynamics on this then I observed that the
temperature kept on rising till about 1500 K. and then it got an error of
v limiit exceed. the input for the dynamics is as follows:

&cntrl
  imin=0,irest=0,ntx=1,ntb=1, cut=10, ntp=0,
  ntr=1, ntc=2, ntf=2, tempi=10.0,temp0=300.0,
  tautp=4.0, ntt=1,
  nstlim=300000, dt=0.001,
  ntpr= 1, ntwx=1000, ntwr=3000,
 &end Group input for restrained atoms (1-12) 10 RES 1 12 END
END

I think it is due to the rise in vdw energy during the minimization.

Any help and suggestions will be of great help.

With regards,

Anshul Awasthi
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India.
Mobile +91-9872220352


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