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Hi, all,
I am trying to do anisotropic coupling using Parrinello-Rahman. I want
to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However, I find
that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, fluctuation is
626 bar for pressure and 11.21 K for temperature.) I run
Shuangxing Dai wrote:
Hi, all,
I am trying to do anisotropic coupling using Parrinello-Rahman. I
want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However,
I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K,
fluctuation is 626 bar for pressure and 11.21 K
Dear gromacs Users,
I found this in the web, but I wanted to know if there exists the
possibility now of using implicit solvent efficiently.
Thanks,
Esteban
A repeating question on the mailing list whether GROMACS can perform
implicit solvent simulations. The answer is, not really. Over the
ithu wrote:
Dear gromacs Users,
I found this in the web, but I wanted to know if there exists the
possibility now of using implicit solvent efficiently.
Implicit solvent will be supported in the upcoming release.
-Justin
Thanks,
Esteban
A repeating question on the mailing list
Hi Chris,
What about:
find . -name *.gro -exec sed -i -e '$q' -e '3,$s/^\(.\{44\}.\).*$/\1/' {} \;
Assuming using a format %8.3f for coordinates and a single frame in
the .gro file. Otherwise things will get more complicated.
Cheers,
Tsjerk
On Sun, Jul 4, 2010 at 12:45 AM,
Hi Ehud,
we recently developed an extended amber99sb forcefield + some scripts which
probably can do exactly what you want (setting up alchemical mutations for any
amino acid mutation except for proline).
We tested it by calculating thermostability differences for a set of 100+
mutations of an
Thanks for the response.
Yes, I know that large fluctuations will be expected. But why the average
was not even correct? Also, how can I reach some state ( some pressre and
temperature) and know/tell that the system is in equilibrium if the average
is not correct with large fluctuation? I mean I
On 05/07/10 16:27, Justin A. Lemkul wrote:
ithu wrote:
Dear gromacs Users,
I found this in the web, but I wanted to know if there exists the
possibility now of using implicit solvent efficiently.
Implicit solvent will be supported in the upcoming release.
Since it interests me too...
Shuangxing Dai wrote:
Thanks for the response.
Yes, I know that large fluctuations will be expected. But why the
average was not even correct? Also, how can I reach some state ( some
pressre and temperature) and know/tell that the system is
in equilibrium if the average is not correct with
Shay: that's a better idea than I had, thanks.
Tsjerk: that's likely as fast as its ever going to get. this is great.
I was initially worried that it would mangle the last line of the .gro in a triclinic box definition, but it seems to be ok.
Thanks all,
Chris.
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What
Hi,
I have run a simulation using gromacs 4.0.7 with 50 copies of amphiphilic
surfactant ( in water) using Martini coarse-grained force-field. Mere
visualization of trajectories shows that starting with 50 discrete copies, they
gradually aggregate and finally two well-separated large micelles
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