Dear Thomas
Very thanks for your attention.
Studying of the script clarified my ambiguities. If I want to do your
tutorial,
1 2 3
__________________
4 5 6
For each transformation and in each substep 1->4, 2->5 and 3->6, I should
do minimization,
equilibration<
http://ambermd.org/tutorials/advanced/tutorial9/equi.in>
and production
<
http://ambermd.org/tutorials/advanced/tutorial9/prod.in>for each
lambda.
I have a question about Running and Analyzing the MD simulations section.
In tutorial, there is
Transformation: Remove charges from BNZ H6 - Medium: Water
Lambda DVDL rms ksteps TEMP rms PRESS rms
Density rms Filename
0.100 -5.424 1.193 100 299.55 5.96 2.8
360.7 0.9842 0.0038 bnz_prod_v0_l1.out
.
.
.
.
.
.
0.900 -7.445 1.308 100 300.14 6.07 4.9
357.4 0.9835 0.0043 bnz_prod_v0_l9.out
You pointed only to bnz_prod_v0_lx.out ( x= 1,2,3,4,5,6,7,8,9) and not to
bnz_prod_v1_lx.out. why?
Are bnz_prod_v0_l1.out file and bnz_prod_v1_l1.out file identical?
Do not need to use bnz_min_v0_l1.out or bnz_equi_v0_l1.out files?
How do you obtain these data from *.out files?
For example, DVDL = -5.424
Best Regards
On Wed, Nov 30, 2011 at 7:50 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > 1) Table in tutorial relates to only one of two transformation you
> > mentioned (transformation of the benzene bound to lysozyme). And table
> > relating to the transformation of the benzene in water is as follows:
> >
> > Process Step 1 Step 2 Step 3
> > V0 bnz bnz phn
> > V1 bnz phn phn
>
> that is correct. The mask, ifsc, crgmask settings stay the same as in the
> complex for the in-water transformation.
>
> > 2) I should use 162 times mpirun -np 2 $AMBERHOME/exe/sander.MPI -ng 2
> > -groupfile *.group for the transformation of the benzene bound to
> > lysozyme and 162 times for the transformation of the benzene in water.
> > Is it true?
>
> You do 2 transformations (in complex and in water) x 3 substeps (charges,
> vdW, charges again) x 9 lambdas x three runs (minimization, equilibration,
> production) so a total of 162 calls to mpirun. The total number is not
> important, e.g. the minimization runs are much shorter than the
> productions and a real study would look different anyway.
>
> > 3) Unfortunately, table in tutorial is unclear for me.
> >
> > Your table (benzene to phenol transformation in bound state) contain 6
> > parts
> >
> > 1 2 3
> > __________________
> >
> > 4 5 6
>
> 1 and 4 are both settings used in step 1 (charge removal). The substep
> uses two different mdin-files. The same goes for 2+5 and 3+6. The overall
> transformation you want is 1->6 but you do it in substeps 1->4 2->5 and
> 3->6 and add their results together.
>
> If you study the prepare_example.bat script that comes with the tutorial
> you will see how the different steps/program calls/input files are all put
> together for the complete run.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
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Received on Sat Dec 03 2011 - 04:30:02 PST
