. David: I am trying to compute diffusion from a trajectory that was
created with iwrap =1. The systems are ~30,000 atoms with box dimensions of
about 65x65x65 (angstroms) and molecular weights around 250 g/mol. My input
file looks like this:
NVE
&cntrl
iwrap = 1,
imin = 0,
irest = 1,
ntx = 5,
nstlim = 10000000,
dt = 0.002,
ntwx = 1000,
ntpr = 10000,
ntb = 1,
ntwr=0,
ntc=2,
ntf=2,
cut = 10,
ntt = 0,
ntp=0,
tempi = 300,
&end
In my ptraj script I did use the image command, but that was after
calculating diffusion and radius of gyration. I was curious to compare
RMSD's with MSD's after I started to struggle with the diffusion. My ptraj
scripts look like this:
trajin ../Ethoxy_0G100.nve.mdcrd
diffusion :DEF average diffDEF.dat 2
diffusion :OAC average diffOAC.dat 2
#diffusion :WAT average diffWAT.dat 2
radgyr :DEF out radgyrDEF.out mass
radgyr :OAC out radgyrOAC.out mass
#radgyr :WAT out radgyrWAT.out mass
##RMSD Part
reference ../Ethoxy_0G100_nve.crd
center :1-2 mass origin
image origin center
rms reference mass out 0G100_rmsd-all.dat :1-2 time 2.0
rms reference mass out 0G100_rmsd-C.dat :2.C1,C2,C3,C4,C5,O5 time 2.0
rms reference mass out 0G100_rmsd-DEF.dat :DEF time 2.0
rms reference mass out 0G100_rmsd-OAC.dat :OAC time 2.0
#rms reference mass out 0G100_rmsd-WAT.dat :WAT time 2.0
.Daniel: I'm having trouble compiling the beta cpptraj - I'm pretty new to
linux and command line stuff so I'm sure that part is just me being slow
but I'll figure it out here eventually.
.Thomas: I just attempted the unwrap command and that totally worked!!
Thanks! I'll be sure to include that from now on. I didn't realize that was
required at first because the diffusion command automatically accounted for
wrapping around in one dimension at a time.
On Tue, Mar 8, 2016 at 5:34 PM, David A Case <david.case.rutgers.edu> wrote:
> On Tue, Mar 08, 2016, Timothy Christopher Schutt wrote:
> >
> > ...one molecule sitting on the box edge or corner happens to cross the
> > boundary in two different dimensions during the same frame change. In
> > this scenario the wrapping of the second periodic boundary is not
> > accounted for and the MSD jumps up by n * L^2/N (L= simulation box
> > length. n= number of molecules in the mask double wrapping that frame,
> > and N = the number of molecules in the mask).
>
> Are you trying to compute diffusion behavior from a trajectory that was
> originally created with iwrap=1? Or that has been subject to the "image"
> or
> "autoimage" command in cpptraj? Just trying to pin down possible sources
> of
> problems.
>
> ....dac
>
>
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Received on Tue Mar 08 2016 - 17:30:03 PST
