Hi,
I try to use umbrella sampling for calculating PMF. i change distance
between protein and ZNS nanosheet. I use gomacsV4.5.4
after minimization and equilibration. i use:
grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
this is md_pull.mdp:
integrator = md
Dear all
I have generated a structure.par file using ffTK toolkit of VMD. To use it
in gromacs I have generated the structure.top file using topoltool plugin
of vmd.
1. Now, how can i generate "itp" file to carry out, protein-ligand
simulation?
2. Will it be sufficient if I generate "gro" file u
Hello,
Thank you Justin and Qinghua!
Can I ask
1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add
a new line of "nstfout=0"?
Yeah, you can add that line, or you can leave it be, the default is set
as ZERO.
2) should I change "nstxout-compressed=5000" to
Thank you Justin and Qinghua!
Can I ask
1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial.
Should I add a new line of "nstfout=0"?
2) should I change "nstxout-compressed=5000" to "nstxout-compressed=5"?
3) Do you mean using "compressed-x-grps=Protein" will set xtc-grp
The sum of the two largest charge group radii (7.984601) is larger than
rlist (0.347900).
the configuration looks fine across pbc. Everything looks normal. Following
is my md. I have user-specified potential so I need to have cut-off values
as given below.
integrator= md
dt
Hello,
Here is the settings I used in the mdp file, you may consider it.
nstxout = 0 ; save coordinates every 2 ps
nstvout = 0 ; save velocities every 2 ps
nstxtcout = 500 ; xtc compressed trajectory output every
2 ps
nstenergy = 50
On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
Hi,
I get this error only in NVT equlibration step, not in the NPT and
production steps. Should I worry about it?
In gromacs page it tell the error can come from 4 reasons, but how I can
recognize which can be mine?
Check the size of your largest
On 12/15/17 5:30 AM, abhisek Mondal wrote:
Hi,
For performing Umbrella Sampling Simulation of protein ligand system
how should one device the proper unbinding path, as in case of biological
systems unbinding paths can be various ?
Few words regarding this issue would be highly appre
On 12/15/17 5:44 AM, Diez Fernandez, Amanda wrote:
Dear users,
I am running many (almost identical) simulations and every so often one crashes
and I get this message. Initially I just deleted everything, started from
scratch and the problem was solved. However it is starting to be annoying.
On 12/15/17 7:34 AM, ZHANG Cheng wrote:
Dear Qinghua,
Thank you very much.
Do you mean set "nstvout" and "nstenergy" as 0?
nstenergy is the frequency of writing energy terms to the .edr file. It
has no effect on the .trr, which is only impacted by nstxout
(coordinates), nstvout (velocitie
Dear Qinghua,
Thank you very much.
Do you mean set "nstvout" and "nstenergy" as 0?
Also, how to set xtc-grps as a group?
The original md.mdp file is:
title = OPLS MD simulation
; Run parameters
integrator = md; leap-frog integrator
nsteps = 1
Hello,
Normally, you don't need to write out the force and velocity, then you
can set nstfout and nstvout as ZERO, then only
the coordinates will be written out in a xtc file.
If you don't care about waters, then you can also set xtc-grps as a
group without waters and counterions.
Best,
Qin
Dear users,
I am running many (almost identical) simulations and every so often one crashes
and I get this message. Initially I just deleted everything, started from
scratch and the problem was solved. However it is starting to be annoying.
Any idea what is happening?
Is it an error of Gromacs
Dear Gromacs,
I am following Justin's tutorial of "Lysozyme in Water" to run the MD.
The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less
frequent intervals.
In the md.mdp file, the "dt = 0.002". My understanding is to change the five
"5000" into "5" to achieve 1
Hi,
For performing Umbrella Sampling Simulation of protein ligand system
how should one device the proper unbinding path, as in case of biological
systems unbinding paths can be various ?
Few words regarding this issue would be highly appreciated.
Please suggest few references (regar
Hi,
I get this error only in NVT equlibration step, not in the NPT and
production steps. Should I worry about it?
In gromacs page it tell the error can come from 4 reasons, but how I can
recognize which can be mine?
http://www.gromacs.org/Documentation/Errors?highlight=documentation#The_sum_of_t
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