Hi All,
I have one quick questions about free energy calculations via pull
code+umbrella sampling. (see below for some further information on what I am
trying)
First of all I think Justin is right umbrella sampling is much more
straightforward. In particular in my situation where I see
After some further search I found this very useful script which converts
xpm to digits. This has solved my problem.
#!/usr/bin/env python
import sys
def unquote(s):
return s[1+s.find(''):s.rfind('')]
def uncomment(s):
return s[2+s.find('/*'):s.rfind('*/')]
def col(c):
color =
Dear Gmx User,
I was running a simulation in Ubuntu 14.0 for 20 ns. I have a total disk
space of 120 GB. I was running the sim from Downloads/Gromacs/build folder.
But after runing 9 ns, the siom stops giving an error message insufficient
disk space. I have check the space it have more than 110
On 2/9/15 8:55 PM, Agnivo Gosai wrote:
Dear Users
Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating
the topology and the itp files. Therein , automatic position restraints are
generated. Now, I have never used manual restrain force constants.
If you're using the
Dear Users
Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating
the topology and the itp files. Therein , automatic position restraints are
generated. Now, I have never used manual restrain force constants.
Could any user suggest any source / literature for choosing
On Mon, Feb 9, 2015 at 12:40 PM, IÑIGO SAENZ
inigo.saen...@estudiant.upf.edu wrote:
Dear Mark,
I've been researching about energy groups and I think that it isn't the
solution for my problems.
The background of my question is the following:
I'm currently working with the people that
Note that perf/W or perf/buck of a certain simulation on a certain
hardware can be quite misleading. Currently we balance CPU-GPU load by
shifting long-range electrostatics work to the short-range kernels.
This involves a tradeoff which does not always give the benefit one
may expect and that's
On 2/9/15 4:11 PM, Agnivo Gosai wrote:
Dear Users
My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's
tutorial advocates a 10 ns simulation time. I found that after running WHAM
, my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my
histograms have two
On 2/9/15 11:00 AM, Agnivo Gosai wrote:
Hi Antara
Did you check the plot of the potential energy against the simulation time
? You can visualize the convergence of your energy minimisation from the
above plot.
Energy minimization, by definition, converges to some value (but there is no
Dear Users
My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's
tutorial advocates a 10 ns simulation time. I found that after running WHAM
, my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my
histograms have two peaks!!
So should I increase the simulation
Hi,
I minimised a heterogenous lipid system of 1464 DOPC and DOPG and applied
position restraints as well as had vdwradii.dat file for genbox step. Yet
after minimisation, there are gaps between the lipid molecules. Pls suggest
a remedy.
--
Regards,
Antara
--
J.R.F.(Project)
Systems Biology
Dear Mark,
I've been researching about energy groups and I think that it isn't the
solution for my problems.
The background of my question is the following:
I'm currently working with the people that develops ACEMD and because of
that I've got access to some information that ACEMD uses for its
Dear Erik,
I have the matrix and I converted it with xpm2ps into a coloured image.
I want to compare the ligands at the same time so I would be interested
in the diagonal.
Which is the best way to get from the xpm matrix the diagonal plotted in 2d
as a function of time and rmsd value?
Best
Dear Gromacs Users,
I want to calculate the rmsd between two ligands - the system is exactly
the same, just the ligand binding conformations are different.
Therefore i want to use g_rms with the option -f2 as in the following
command:
g_rms -f trajout.trr -f2 ../2/trajout.trr -n -o
In g_rms
On 2/8/15 5:53 PM, Alexander Law wrote:
This method doesn't work. Does each simulation have to complete the 10 ns in
order to move on the analysis step, or can I use incomplete simulations?
Analyze however much time you like.
If not, is there another possibility to force the simulations
On 2/9/15 7:34 AM, Antara mazumdar wrote:
eRROR OBTAINED DURING NVT:
Water molecule starting at atom 673675 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
NVT CONDITIONS WERE :
n for B2AR-POPC system
define = -DPOSRES ; Protein is
Dear Experts and users,
I am running simulation for solvation free energy calculation using
thermodynamic integration approach (as mentioned in Justin's tutorial). My
system consist of a cation molecule, an anion molecule and bulk of solvent
molecules.
I want to understand the pH of my system,
On 2/9/15 7:41 AM, Antara mazumdar wrote:
i got the following result after EM of this system of mine.
writing lowest energy coordinates.
Steepest Descents converged to Fmax 1000 in 15280 steps
Potential Energy = -5.0853170e+06
Maximum force = 9.9438867e+02 on atom 179440
Norm of force
eRROR OBTAINED DURING NVT:
Water molecule starting at atom 673675 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
NVT CONDITIONS WERE :
n for B2AR-POPC system
define = -DPOSRES ; Protein is position restrained (uses the
posres.itp file
i got the following result after EM of this system of mine.
writing lowest energy coordinates.
Steepest Descents converged to Fmax 1000 in 15280 steps
Potential Energy = -5.0853170e+06
Maximum force = 9.9438867e+02 on atom 179440
Norm of force = 7.8095098e+00
Should i go ahead with
On 2/8/15 6:08 PM, Agnivo Gosai wrote:
Dear Users
I am using g_hbond to get the H-bonds for a particular simulation over the
entire trajectory. In the log file I can find which reesidues are forming
H-bonds.
However , I want the H-bonds formed over the entire simulation length frame
wise or
On 2/9/15 5:07 AM, Antara mazumdar wrote:
Hi,
I minimised a heterogenous lipid system of 1464 DOPC and DOPG and applied
position restraints as well as had vdwradii.dat file for genbox step. Yet
after minimisation, there are gaps between the lipid molecules. Pls suggest
a remedy.
Dear Julian,
Use the -m flag.
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 9 Feb 2015, at 12:20, Julian
On 2/9/15 7:42 AM, vivek sharma wrote:
Dear Experts and users,
I am running simulation for solvation free energy calculation using
thermodynamic integration approach (as mentioned in Justin's tutorial). My
system consist of a cation molecule, an anion molecule and bulk of solvent
molecules.
I
Dear Julian,
I see no other means than writing a script to parse out the diagonal. The xpm
format is quite human readable so I don’t think it will take you long to figure
out how to do.
Kind regards,
Erik
On 9 Feb 2015, at 14:16, Julian julim...@gmail.commailto:julim...@gmail.com
wrote:
Juilan,
A quick way to do this is with an awk script, such as:
awk '{print $NR}' (your matrix.dat file here). This will print the diagonal of
the matrix. If you want the one from the .xpm file you need to use something
like:
awk '{if($0!~/*/){print substr($0,counter+2,1),counter++}}' Though
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