For a one command line in bash I would use
printf "r 1-442 \n q \n" | command
In echo it is similar but you need to work out the " and ' very carefully.
Cheers,
On Mon, 11 Feb 2019, 17:21 ZHANG Cheng <272699...@qq.com wrote:
> Dear Pedro Deira,
>
>
> Sorry, could you please show me how to
Dear all,
I really wanted someone to help me.
I'm analyzing the output files g_energy -vis (evisco.xvg and eviscoi.xvg files).
These files contain 5 columns, among which the first seems to be the
time, but what are the other 4?
Thank you!
Regards,
*Neila Cristina Fonseca Machado*
*Ph.D.
Dear Pedro Deira,
Sorry, could you please show me how to include the newline using "echo" with
only one command line?
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Feb 11, 2019 06:36 AM
To:
Hi,
Like
echo "r 1-442\nq" | gmx make_ndx -f equilibration.gro
The "\n" is the code for a new line.
Mark
On Mon, 11 Feb 2019 at 18:22 ZHANG Cheng <272699...@qq.com> wrote:
> Dear Pedro Deira,
>
>
> Sorry, could you please show me how to include the newline using "echo"
> with only one
Dear use 43a1 extended phosphorylated force field. Although phosphorylated
amino acids are not in the active site or not involved in the interaction
with ligand but in broad context these phosphorylated residues have impact
on structure of protein over the function of time
On Mon, Feb 11, 2019,
Hello. try:
echo -e "r 1-442\nq\n" | gmx make_ndx -f equilibration.gro
If this does not work, try:
gmx make_ndx -f equilibration.gro<
Hello,
I'm sorry I don't think I understood fully, so just as a clarification. Is
it possible to go from 0 through 21? If so, which line of the mdp file do I
change so that it will recognize the full range?
Thank you so much,
Angelina Malagodi
On Sun, Feb 10, 2019 at 3:03 AM Mark Abraham
Please don't reply to the whole digest, just cut and paste the relevant
portions and change the subject (or better, don't subscribe in digest
mode when actively participating in discussions).
On 2/10/19 1:48 PM, James wrote:
Hi Justin,
Thank you for the information. This is a bit
On 2/11/19 3:05 PM, Angelina Malagodi wrote:
Hello,
I'm sorry I don't think I understood fully, so just as a clarification. Is
it possible to go from 0 through 21? If so, which line of the mdp file do I
change so that it will recognize the full range?
There are 21 states. The first state
What about the other checks I suggested? IS the failing test 100%
reproducible with AVX_512?
--
Szilárd
On Mon, Feb 11, 2019 at 9:15 PM David Lister wrote:
>
> Hello,
>
> My bad, I copied my single precision build by mistake, this is what was
> used originally for double precision:
>
> cmake ..
On 2/11/19 9:26 AM, Edjan Silva wrote:
Dear,
I was not successful running the following command:
$ gmx rmsdist *-s* md_0_1.tpr -*f* md_0_1.xtc *-o *rmsdist.xvg
GMX displays the following error:
---
Program: gmx rmsdist, version
Hello,
My bad, I copied my single precision build by mistake, this is what was
used originally for double precision:
cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -DGMX_DOUBLE=on
On 2/10/19 12:26 PM, marzieh gharouni wrote:
Hello
I want to do noPeriodic Boundary Conditions for my system.
Gromacs tutorial has said that it can not be used the center and nojump in
one command simultaneously.
I would be grateful if you could explain the reasons for it?
Both apply
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
Dear,
I was not successful running the following command:
$ gmx rmsdist *-s* md_0_1.tpr -*f* md_0_1.xtc *-o *rmsdist.xvg
GMX displays the following error:
---
Program: gmx rmsdist, version 2019-beta3
Source file:
Dear all,
I have been trying to obtain opls forcefield for small molecules.
On previous discussions I have red that one possibility is to use the
Schröedinger ffld server in combination with ffconv.py script to generate the
topology.
Unfortunately the link for the ffconv.py link is expired
Dear all,
I have been trying to obtain opls forcefield for small molecules.
On previous discussions I have red that one possibility is to use the
Schröedinger ffld server in combination with ffconv.py script to generate the
topology.
Unfortunately the link for the ffconv.py link is expired
Harry,
That does not seem normal. Have you tried to run on CPU-only and see
if that reproduces the issue (e.g. run mdrun -nsteps 0 -nb cpu -pme
cpu a few times).
--
Szilárd
On Mon, Feb 11, 2019 at 11:25 AM Harry Mark Greenblatt
wrote:
>
> BS”D
>
> Dear All,
>
> Trying to run a system with
Dear all,
I am working with a protein having phosphorylated serine and threonine
residues. I will be performing ligand-protein MD. These phosphorylated
amino acid residues are not located in the active site of protein.
Should I just replace the phosphorylated serine and threonine residues with
Dear all,
I am working with a protein having phosphorylated serine and threonine
residues. I will be performing ligand-protein MD. These phosphorylated
amino acid residues are not located in the active site of protein.
Should I just replace the phosphorylated serine and threonine residues with
Hi James,
hydrogen bonds are an intrinsically quantum phenomenon, and are more
like a partial covalent bond than anything else. (According to NMR
experiments. Polarisation is transfered across H-bonds).
The good news is that for most purposes MD water "just works". Even
though the exact
BS”D
Dear All,
Trying to run a system with about 70,000 atoms, including waters, of a
trimeric protein. Went through minimization, PT and NPT equilibration.
Most of the time, it starts and runs fine. But once in about 5 tries, I get:
12500 steps, 25.0 ps.
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