Hi,
On Thu, May 8, 2014 at 10:04 AM, Valentina Romano
<valentina.romano.unibas.ch> wrote:
> First of all, I minimized the system in 2 steps.
> 1) only solute restrained
> 2) all atoms free
> The input file for the 2nd step is:
>
> &cntrl
> imin=1,
> maxcyc=10000,
> ncyc=2500,
> ntb=1,
> igb=0,
> cut=12
> /
You don't say what input you used for the MD stage, but explicit
solvent simulations in general require more careful minimization than
implicit solvent sims. For example, what I usually do is after an
initial minimization with relatively strong positional restraints on
solute heavy atoms, my second stage will be a short (15 ps) NVT MD
simulation with the same restraints using a 1 fs timestep to let the
water relax, followed by more minimization with gradually decreasing
restraints. I then switch to a series of short NPT simulations with
gradually decreasing restraints on solute to allow the density to
start to equilibrate. If you post your actual MD input we could make
more specific recommendations.
> I think the error is related to the minimized structure I am using as input.
> Is there a way to check if the minimization went well (e.g.: an easy way to plot the total energy vs time steps)?
> How to check if it necessary minimize for a longer or shorter time?
I think that MdoutAnalyzer.py will let you plot energy terms from
MDOUT output relatively easily. Alternatively you could read MDOUT
data in with cpptraj (i.e. 'readdata <mdout>'), then write whatever
terms you want to the file format of your choice with 'writedata'. In
general you want to pay attention to your gradient - if it's not
relatively flat for your last steps you probably could do with
additional minimization. Alternatively you may want to try using the
XMIN minimizer in sander (ntmin = 3).
Good luck,
-Dan
>
> The last step of the minimization is the following:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10000 -1.0588E+05 6.6968E-01 7.0286E+01 N9 3834
>
> BOND = 7509.5321 ANGLE = 683.5019 DIHED = 2272.1178
> VDWAALS = 17150.2089 EEL = -143037.0880 HBOND = 0.0000
> 1-4 VDW = 785.8019 1-4 EEL = 8760.7170 RESTRAINT = 0.0000
>
> While the enrgy at the step 0 of the MD is:
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = -113244.2583 EKtot = 0.0000 EPtot = -113244.2583
>
> Could the difference in the energy values had influenced the error I got? If yes, I can solve it?
>
> Thank you
> Valentina
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 08 2014 - 09:30:06 PDT
