Dear Thomas,
I think it is true in the case of data similarity.
However my results seem to be similar, but I guess my RMSF sets are
different significantly in some residues in each simulation.
Is it still normal to have such variation is some residues?
Thanks for reply,
Regards,
M. Reza
On Wed, May 26, 2010 at 5:27 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> others may correct me, but I see little use in conducting thousands of
> minimization steps right before an MD simulation. This is merely
> equivalent to starting your MD run from structures that are at e.g. 0.1,
> 0.01 or 0.001 K, just to heat them up to 300 K right afterwards. The
> differences you see in the three simulations should be the normal
> variation of MD runs starting from different (if very similar) initial
> structures.
>
> I normally do 100-500 minimization steps, just to get rid of bad contacts.
> In my experience that is more than sufficient.
>
> Kind Regards,
>
> Thomas
>
> On Wed, May 26, 2010 8:41 am, M. Reza Ganjalikhany wrote:
> > Hello all,
> >
> > I have problem with adjusting the number of minimization steps for my MD
> > simulation.
> > I ran 3 MD simulations in explicit solvent with a protein containing 181
> > a.a. for 2 nanosec and I got
> > 3 different sets of data in which the RMSd, RMSf, radius of gyration and
> > other data were a bit different in each one!!
> >
> > Minimization steps were adjusted as below:
> > run #1 : 2500 steps (1000steps steepest decent+1500 steps conjugate
> > gradient)
> > run #2: 5000 steps (2000 steps steepest decent+3000 steps conjugate
> > gradient)
> > run #3 :10000 steps (2000 steps steepest decent+8000 steps conjugate
> > gradient)
> >
> > Is it normal to obtain different sets of data upon doing different
> > minimization steps?
> > How many minimization steps should be sufficient? How is it possible to
> > find
> > ot its suficiency?
> >
> > Data related to radius of gyration, rmsd and rmsf are attached as
> > pictures.
> >
> > Thanks in advance,
> > M. Reza
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> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Wed May 26 2010 - 06:30:10 PDT
