Thank you very much Dr. Daniel R. Roe your suggestion worked and this was a format issue.RegardsVahid
On Thursday, August 6, 2015 5:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
You used ioutfm=1, so your trajectory is in NetCDF format. Use that format
when opening it in vmd. Hope this helps,
-Dan
On Thursday, August 6, 2015, Vahid Kshani <vahid_edu.yahoo.com> wrote:
> 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
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Aug 07 2015 - 00:30:02 PDT
