On Thu, May 15, 2014 at 7:07 AM, Valentina Romano
<valentina.romano.unibas.ch> wrote:
> BOND = 7906.5852 ANGLE = 529.6831 DIHED = 2310.5740
> MD
>
> BOND = 120.7537 ANGLE = 529.6831 DIHED = 2310.5740
>
This appears to be your problem: your bond energy jumps from 7906.5852
to 120.7537. All of your other energy components are the same. Are you
sure you are using the same topology file?
-Dan
>>What are your starting velocities? You have a temperature of 508K at step
>>2 of the MD run. And you already have potential energy that is 10,000
>>kcal/mol higher than in the minimization. You need to try to track down
>>where such difference are coming from.
>
> The input file for the MD was:
>
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
> ig=-1,
> ntb=1,
> ntr=1,
> cut=10,
> ntc=2,
> ntf=2,
> tempi=300.0,
> temp0=300.0,
> ntt=3,
> gamma_ln=5.0,
> nstlim=15000, dt=0.001,
> ntpr=1, ntwx=1, ntwr=1000
> restraint_wt = 10.0,
> restraintmask=':1-246.CA,C,O,N | .3834-3843'
>
> Since I want to relax in a NVT ensemble solvent molecules of the structure previously minimized, might be more correct set irest=1 and ntx=7?
>
>
> Vale
>
>
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Thu May 15 2014 - 09:00:05 PDT
