O.K cheers Chris. I do intend to equilibrate the system at the desired
temperature before constructing the histogram.
chris.ne...@utoronto.ca wrote:
> Depending on your system and chosen thermostat, gen-vel=no can be a
> dangerous idea (very small original velocities simply get scaled up);
> beside
Depending on your system and chosen thermostat, gen-vel=no can be a
dangerous idea (very small original velocities simply get scaled up);
besides, you should be able to equilibrate from a gen-vel=yes pretty
quickly. I don't disagree with Justin's comment, but just because it
works doesn't m
Many thanks
Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> I am not using periodic boundary conditions for the simulations. I may
>> have sorted it out now. I was generating velocities in the umbrella.mdp
>> file, I have since set gen_vel = no, and the histogram has the corr
Gavin Melaugh wrote:
Hi Justin
I am not using periodic boundary conditions for the simulations. I may
have sorted it out now. I was generating velocities in the umbrella.mdp
file, I have since set gen_vel = no, and the histogram has the correct
shape (should this make a difference?)
If you
Hi Justin
I am not using periodic boundary conditions for the simulations. I may
have sorted it out now. I was generating velocities in the umbrella.mdp
file, I have since set gen_vel = no, and the histogram has the correct
shape (should this make a difference?)
Cheers
Gavin
Justin A. Lemkul wr
Have you watched the trajectory? That will show you what your pull group is
doing. Is this a periodicity effect? It should be fairly obvious iff the sign
of dX, etc flip-flops in the pullx.xvg file.
-Justin
Gavin Melaugh wrote:
Thanks Chris and Justin
I do get the output I want from gro
Thanks Chris and Justin
I do get the output I want from grompp(below). The distance of 5.507 nm
is the distance that I want to start with and I assume it is therefore
the equilibrium distance for the harmonic potential. The COM distances
from the simulations fluctuate around this value which is wh
I missed that pull_start = yes, sorry. So Gavin, your run should have
stayed around the starting position. Make the histogram directly and
you should get a better idea.
Chris.
-- original message --
To clarify, the tutorial sets "pull_init1 = 0" because it is used in
conjunction
with "p
Gavin Melaugh wrote:
Hi Chris
Thanks very much for your help. The reason I used pull_init1 = 0 is
because this is the value that is used in the tutorial. Maybe I am
misinterpreting its meaning. In the tutorial it says that you do not
have to specify a value separately for each configuration. I
Gavin,
I think it's time for you to read some papers and read the gromacs
manual pull COM section. A few days of reading will make all of this
clear to you.
-- original message --
Hi Chris
Thanks very much for your help. The reason I used pull_init1 = 0 is
because this is the value that i
Hi Chris
Thanks very much for your help. The reason I used pull_init1 = 0 is
because this is the value that is used in the tutorial. Maybe I am
misinterpreting its meaning. In the tutorial it says that you do not
have to specify a value separately for each configuration. I am now
thinking that in
Gavin, let's take g_wham out of the picture for now to simplify
things. First, you umbrella is pretty strange. You want them to have a
distance of 0.0 nm (pull_init1 = 0)???
So let's look at making a histogram from your raw data.
1. cat pullx.xvg |awk '{print sqrt($1,$5*$5+$6*$6+$7*$7)}' > m
Hi Guys
I am having great difficulty generating a histogram of the correct shape
from g_wham. I am running umbrella sampling on one configuration fo two
molecules at a fixed distance using the following
pull parameters. ( I am just running one configuration to begin with so
that can make sure that
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