Dear all
we are running a MD simulation on a protein-drug complex in a rectangular water box, the complex was minimized with periodic boundaries.
The starting energy is 7.1251E+10 and the final energy after minimization is -2.3292E+05
The initial structure and the minimized structure has 0.58 ang deviation.
unfortunately vmd does not read the mdcrd files generated after Heating (file size:140MB) and Equilibration (file size 818MB) and when we try opening mdcrd files using text editor error is "too much binary data".
However when we convert the rst files to pdb, visualization is successful and the structure seems to be fine.
LIST OF INPUTS
1) minimization:
Minimization to relax initial bad contacts, explicit solvent
&cntrl
imin=1,
ncyc=1000,
maxcyc=5000,
ntpr=50,
cut=8,
restraintmask='!:WAT&.CA,C,O,N'
restraint_wt=10.0,
/
2) Heat:
Explicit solvent initial heating mdin
&cntrl
imin=0, irest=0, ntx=1,
ntpr=1000, ntwx=1000, nstlim=200000,
dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=8, ntb=1,
iwrap=1, ioutfm=1, nmropt=1,
/
&wt
TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
VALUE1=10.0, VALUE2=300.0,
/
&wt TYPE='END' /
3) Equilibration:
Explicit solvent molecular dynamics constant pressure MD
&cntrl
imin=0, irest=1, ntx=5,
ntpr=1000, ntwx=1000, nstlim=2000000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=1.0, ig=-1,
ntp=1, ntc=2, ntf=2, cut=8,
ntb=2, iwrap=1, ioutfm=1,
/
I would appreciate your comments on the issue.
Regards
Vahid
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 06 2015 - 04:30:02 PDT
