I also checked the output of the minimization:
Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.81875038188621e+04
Maximum force = 3.20769543152855e+02 on atom 331
Norm of force = 2.04356801849931e+01
I assu
Dear all,
I am trying to simulate a GB simulation of a 112 amino acid long protein. I
keep getting these errors,
Step 27718, time 55.436 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
Dear all,
I did another simulation with only SPC water. Then I used the local pressure
gromacs to calculate the stresses. It seems to be reasonable.
I am not sure how to figure out what goes wrong with my previous simulations
when plugged into the local pressure gromacs.
Could someone help me in
Thank you Mark, I really appreciate it.
-- original message --
On 20/06/2011 1:23 AM, chris.neale at utoronto.ca wrote:
Dear Mark:
Now I am confused. Your first post indicated that P-LINCS did the
angle constraints. But here you indicate that the v-site algorithm
does it.
No... my second
On 20/06/2011 1:23 AM, chris.ne...@utoronto.ca wrote:
Dear Mark:
Now I am confused. Your first post indicated that P-LINCS did the
angle constraints. But here you indicate that the v-site algorithm
does it.
No... my second email observed that LINCS warnings can result when
v-sites are being
Dear Mark:
Now I am confused. Your first post indicated that P-LINCS did the
angle constraints. But here you indicate that the v-site algorithm
does it. This is probably because my first post was incomplete about
the method that I used.
Can you please confirm my current understanding?
Th
On 19/06/2011 11:44 PM, vidhya sankar wrote:
Dear Justin, Thank you for your previous reply
Dear Justin I used g_hbond tool i have got .xvg
file In that file there are three column The second and third colum
represents What ?.
Which column represents total no of Hbonds t
Dear Justin, Thank you for your previous reply
Dear Justin I used g_hbond tool i have got .xvg file In
that file there are three column The second and third colum represents What ?.
Which column represents total no of Hbonds throught the entire trajectory and
which Columns
Of course you did... Though mind the brackets :)
C_ij = / sqrt ( * )
The point I want to make is that you can easily take the output from
g_covar -ascii and turn it into a correlation matrix. In R
(r-project.org) there is even a dedicated function for it:
x <- scan("covar.dat")
x <- matrix(x,
Hi,
Thats actualy that i did here [1]. Extracting coordinate for every atom
in interesting two group and computing
C_ij = / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j
is vectors
[1]
http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl
On S
Hey,
The method from Lange is quite a different thing. It includes
non-linear correlations, which is interesting to look at for overall
correlation between atoms. If the ultimate goal is to do PCA on it,
then it will give you awkward components that will give you a hard
time trying to interpret.
Hi.
There is two possibilitys
1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that
compites
general corelation coefficients
2. My utility that computes pearson correlation coefficients [2]
[1]
http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.h
On 19/06/2011 6:34 PM, Chathurika Abeyrathne wrote:
Hi,
Is this software compatible with windows 7.
Yes, but its not really a desirable platform for serious computation.
See http://www.gromacs.org/Downloads/Installation_Instructions/Windows
for instructions to build it.
Mark
--
gmx-users
Hi,
Is this software compatible with windows 7.
Thanks.
Regards,
Chathurika.
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