Average Velocity and How to choose Right Alias

From: abhijit ramachandran (abhi_adroit_at_yahoo.com)
Date: Thu Aug 07 2008 - 16:13:06 CDT

Hi all,

I had two questions:

1). Averrage Velocity of DNA in each frame.

I am trying to obtain the average velocity in each frame of my simulation so i added the commands

velDCDfile runvs
velDCDfreq 100

but i dont know how to perform the post analysis, such that i can obtain the average velocity from these files for each frame. Any other method if available then kindly suggest.

2). How to choose Right Alias

The PDB file for the DNA in the bionanotechnology tutorial uses the atom names different from those mentioned in the topology files, so how can i make out which is the alias of what,

eg:

ATOM 1 H5T ADE A 1 -8.309 0.247 -1.545 1.00 0.00 ADNA
ATOM 2 O5' ADE A 1 -7.949 -0.574 -1.102 1.00 0.00 ADNA
ATOM 3 C5' ADE A 1 -7.715 -1.582 -2.103 1.00 0.00 ADNA
ATOM 4 H5' ADE A 1 -6.993 -1.267 -2.720 1.00 0.00 ADNA
ATOM 5 H5'' ADE A 1 -8.590 -1.851 -2.505 1.00 0.00 ADNA
ATOM 6 C4' ADE A 1 -7.168 -2.840 -1.457 1.00 0.00 ADNA
ATOM 7 H4' ADE A 1 -7.388 -3.645 -2.008 1.00 0.00 ADNA

The names H5T or H5'' are not there in the topology file so how do i use the pdbalias command to assign the right alias, i mean is there any way to find it out. I am asking this since i was not able to generate correct psf file using psfgen.

Thanks in advance.

Regards,

Abhijit Ramachandran.

UTA

Script:

#config file
run 10000
structure pore+dna.psf
coordinates pore+dna.pdb
outputName run0s
XSTfile run0s.xst
velDCDfile runvs
velDCDfreq 100
 
bincoordinates eq2.coor
binvelocities eq2.vel
extendedSystem eq2.xsc
 
langevin on
langevinDamping 20
langevinTemp 295
langevinHydrogen off
 
switching on
switchDist 10
cutoff 12
pairlistdist 14
margin 3
 
binaryOutput yes
binaryRestart yes
 
parameters cornell.prm
parameters par_silicon_ions_NEW5.inp
paraTypeCharmm on
wrapAll yes
wrapNearest yes
COMmotion no
 
outputEnergies 100
outputTiming 100
xstFreq 100
dcdFreq 100
restartFreq 100
 
timestep 0.5
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20
 
Pme on
PmeGridSizeX 48
PmeGridSizeY 48
PmeGridSizeZ 96
 
exclude scaled1-4
1-4scaling 1
 
constraints on
consKCol B
consref siliconRest_50.0.pdb
consKFile siliconRest_50.0.pdb
 
## electric field
eFieldOn on
eField 0.0
0.0 150.0

      

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