Hi people,
I'm trying to calculate water self-diffusion coefficient in a solvated DNA
simulation, at NVE ensemble.
I have found that, due to the presence of solute, D is smaller than in bulk
water. Then, I want to compute how much it is smaller, by comparing its
value with respect to a radial distance from the DNA molecule.
I was reading the manual to find a way to put a mask for the water molecules
in order to compute only the ones that are closer to the DNA, but none of
them worked.
trajin 1D20_wat_tip3pfNVE310.x 1 99999
diffusion (:1-20<:5.0)&:WAT 0.1 average 310_within5a
diffusion :WAT&(:1-20>:8.0) 0.1 average 310_without8a
However, it seems that the mask is not selecting the expected atoms, as can
be seem from the output:
PTRAJ: diffusion (:1-20<:1.0)&:WAT 0.1 average 310_within5a
PTRAJ: diffusion :WAT&(:1-20>:8.0) 0.1 average 310_without8a
PTRAJ: diffusion :Na+ 0.1 average Na+310
Mask [:Na+] represents 18 atoms
[No output trajectory specified (trajout)]
1D20_wat_tip3pfNVE310.x: 10000 frames.
Also the value of the diffusion coefficient is the same independently of the
applied mask.
Then I tried the analyze timecorr facilty but it seems that it's not what I
want....
This is the script for the time correlation. :1-20 is the DNA . Trajectories
are saved every 0.1ps.
trajin 1D20_wat_tip3pfNVE310.x
vector a1 :1-20 corr :WAT out vector
analyze timecorr vec1 a1 vec2 a1 out a1.out tstep 0.1
any suggestions would be very helpful.
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Mon Sep 19 2011 - 15:00:02 PDT
