Hello,Pawel,
Thank you for your attention.
I want to compare with the amber force field result of this
paper(Simulations of a protein crystal with a high resolution X-ray
structure: Evaluation of force fields and water models),so I want to
compute all using the same method.
1. if the "bfac_lat_calpha" in figure8 are calculated using a different
approach than the one used in BasicAnalysis, how can I do it?
2. Before running SplitTrajectory.py, I can make sure in each frame of
my trajectory the center of mass of the entire supercll is exactly
aligned with the center of mass of the supercell, because I do this
ctraj.translate.in step (this is done in the BasicAnalysis.sh script
)and I also see that the first asymmetric unit in my supercell produced
from original PDB asymmetric unit coordinates has exactly the same
coordinates as the PDB.
3. I use vmd to open the individual trajectories named "**_**.nc"
gained by running SplitTrajectory.py or "RevSym_**_**.nc" gained by
running RevSym_netcdf.py and original asymmetric unit(asu.pdb), they are
aligned .
4. I do the same MD as this paper. Restrained equilibration began in the
constant-volume ensemble and then transitioned into the
constan-pressure ensemble.So as you said, I need to rescal coordinates.
However, after reading this paper I am confused that wether only
computing the lattice property (for example:rmsd_latt and
bfactor_latt)need rescal coordinates but computing the other
property(like rmsd_ASU ,bfactor_ASU and Distance deviation matrices)
needn't rescale the coordinates?
thank you very much!
Best wishes!
Aimee Li
the ctraj.translate.in:
translate trajectory so centers of mass aligned with pdb crystal
cat <<EOF > ctraj.translate.in
parm ${SC_PRMTOP}
trajin ${SC_TRAJECTORY}
trajout fit.nc netcdf
reference ${SC_RST7}
rmsd reference '!.H=' norotate nofit out drift_nofit.dat
rmsd reference '!.H=' norotate out drift.dat
go
my md.in:
production for complex
&cntrl
imin=0,
dt=0.002,nstlim=5000000,
ntb=2,
irest=1,ntx=7,
ntf=2,ntc=2,
ntp=2,pres0=1.0,ig=-1,
ntt=2,vrand=1000,tempi=287.0,temp0=287.0,
ntpr=1000,ntwr=1000,ntwx=1000,
cut=9.0,
&end
On 10/15/2013 12:04 AM, Pawel wrote:
> Hi Aimee,
>
> Without seeing your data directly it is hard to tell what could be
> happening. Having said that, a few comments,
>
> 1. Your general interpretation of Figure 8 referring to "bfac_lat" and
> Figure 9 to "bfac_asu" is correct. However:
>
> 2. The BasicAnalysis.sh script you are using was written after the paper
> you are referring to, so the analysis is not directly comparable. In
> particular, the "bfac_lat_calpha" in Figure 8 where calculated using a
> different approach than the one used in BasicAnalysis. In general,
> BasicAnalysis is still just a prototype, not documented, and requires
> some work before an official release is made.
>
> 3. Before running SplitTrajectory.py make sure that in each frame of
> your trajectory the center of mass of the entire supercell is exactly
> aligned with the center of mass of the supercell produced from the
> original PDB asymmetric unit coordinates (i.e. a supercell where one of
> the asymmetric units has exactly the same coordinates as the PDB).
>
> 4. After RevSym_netcdf.py, visually inspect the individual trajectories
> in the revsym directory to see if they are aligned with the original
> asymmetric unit. I usually add a frame to my trajectory which has the
> supercell created from the original pdb coordinates. When you run
> RevSym_netcdf.py, each of the asymmetric units from this frame should
> align perfectly with the original PDB. If not, there is an error either
> with how the centers of mass are being aligned or with how the symmetry
> operations are being applied.
>
> 5. You mention "all atomic positions haven't rescaled at any steps. " If
> you were running a constant pressure simulation you want to make sure
> you are rescaling coordinates to account for fluctuations in the box
> size at each step.
>
> Hope these ideas point you in the right directions. Let us know if you
> have questions,
> Pawel
>
>
>
>
> On 10/14/2013 07:36 AM, Yongxiu Li wrote:
>> Dear everyone,
>> I want to construct the unit cell as the tutorial13 and do the
>> same work as the David A. Case's paper "Simulations of a protein
>> crystal with a high resolution X-ray structure: Evaluation of force
>> fields and water models." /J. Phys. Chem. B/ *114*:12811-12824.
>> Different from the paper, we construct the simulation Cell from 108
>> individual unit cells
>> in a 3*3*3 arrangement and simulate the system for 150ns using amber
>> FF99SB force field and TIP3P water.
>> After simulation, I use the 'BasicAnalysis.sh' script in
>> AmberTools/src/xtalutil/Analysis to do each step analysis. Each step
>> is the same as BasicAnalysis.sh but all atomic positions haven't
>> rescaled at any steps. After many steps' analysis, we use the
>> 'analyse_revsym.py' to analyse the last 100ns bfactor . I understand
>> that figure8 is the bfac_lat_calpha.dat in this script and figure9 is
>> the bfac_asu_calpha.dat . I want to know whether I misunderstand to
>> distinguish this two figure and their analysis script . Compared with
>> figure8 in Case's paper,why the bfac_lat_calpha.dat which I gained is
>> so big.
>>
>> the scipt is that :
>> Because the paper said in figure9 the atomic fluctuations were
>> computed on the basis of the distribution of each atom obtained after
>> optimal quaternion alignments of the protein backbones. I do a little
>> modification in ctraj_bfactor_asu(rms reference mass :1-64&!(.H=)
>> changed to rms reference mass :1-64.CA,C,N).
>> Best wishes!
>> Aimee Li
>>
>> In the attachmet, amber-3-3-3.png is the bfactor. and figure 8 and
>> figure9 are the pictures in Case's paper.
>> next two script are using to compute the bfactor.
>> ctraj_bfactor_asu:
>> parm asu.prmtop
>> trajin RevSym_01_01.nc 25001 75000
>> trajin RevSym_01_02.nc 25001 75000
>> ......
>> trajin RevSym_27_03.nc 25001 75000
>> trajin RevSym 27_04.nc 25001 75000
>> reference AvgCoord_asu.rst7.1
>> rms reference mass :1-64.CA,C,N
>> atomicfluct out bfac_asu_calpha :1-64.CA byatom bfactor
>> atomicfluct out bfac_asu_sdch :1-64&!(.H=,CA,C,O,N) byres bfactor
>> atomicfluct out bfac_asu_bkbn :1-64.CA,C,N byres bfactor
>> atomicfluct out bfac_asu_all :1-64 byres bfactor
>>
>> and ctraj_bfactor_lat:
>> parm asu.prmtop
>> trajin RevSym_01_01.nc 25001 75000
>> trajin RevSym_01_02.nc 25001 75000
>> ......
>> trajin RevSym_27_03.nc 25001 75000
>> trajin RevSym 27_04.nc 25001 75000
>> atomicfluct out bfac_lat_calpha.dat :1-64.CA byatom bfactor
>> atomicfluct out bfac_lat_sdch.dat :1-64&!(.H=,CA,C,O,N) byres bfactor
>> atomicfluct out bfac_lat_bkbn.dat :1-64.CA,C,N byres bfactor
>> atomicfluct out bfac_lat_all.dat :1-64 byres bfactor
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Oct 15 2013 - 06:30:02 PDT
