Hi,
In MD simulation the initial velocity is generated by the Maxwell
distribution..Therefore in nvt equilibration we generate the velocity by
keeping gen-vel= yes. In the next equilibration step or production md step
the generated velocity is read by .cpt file. Therefore if we do
continuation =
Dear Users,
I use gmx wham to calculate potential of mean force for multiple systems. I use
the same command for all the simulations, however, in some cases I get
pmfintegrated.xvg and sometimes it is not in the directory. Is it sort of a bug
or there is a technical reason for it?
Thanks,
Dear All,
I start my MD simulation from a previous run using data in tpr and cpt
files
with changed mdp options for the new simulation.
Is it really important to use "continuation = yes" for the lincs
constraints.
What can be wrong if I don't (I use continuation = no).
Best wishes,
Dawid
Hi,
We don't have any useful information to go on, but I'll guess that you've
edited the file e.g. on Windows using a not-very-suitable editor and the
line endings are no longer recognizable elsewhere. Try converting the file,
e.g. with the dos2unix utility.
Mark
On Mon, 5 Aug 2019 at 16:13,
Dear Paul,
thanks for suggestions. Following them I managed to run 91 ns/day for the
system I referred to in my previous post with the configuration:
gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 -gputasks
111 -pin on (still 28 threads seems to be the best choice)
and 56
Dear Dr. Spoel,
I understand that pressure here is the stress tensor with 6 components
(PRESS-XX, PRESS-YY, PRESS-ZZ, PRESS-XY, PRESS-YZ, PRESS-XZ in 6
dimensions), but I'm not sure if it is the per-atom stress tensor (averaged
for all atoms), or the stress of the whole system?
And for the
Dear Justin,I studied your tutorial entitle "Free Energy Calculations: Methane
in Water", Is it based on Thermodynamic integration (TI) methods? I want to
know how to calculated free energy based on perturbation theory? I have a drug
with a carrier at water medium and I want to calculate free
Dear users,
I want to simulate a normal protein-water system by using gromacs
tutorial. when i run this command, gmx pdb2gmx -f inputfile.pdb -o
outputfile.gro , i get this error ; An input file contains a line longer
than 4096 characters, while the buffer passed to fgets2 has size 4096.
Hi everyone
I have a water-protein simulated system. I want to calculate MSD within a
cutoff, that thing how can I solve in gromacs. Can anyone help regarding
this?
Thanks,
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Hi
The number of particles in .gro file and .Top file is not same...Because
you didn't add ligand topology to the topol.top...Check carefully..it's
very basic problem...
On Mon 5 Aug, 2019, 3:57 PM GAYATHRI S, wrote:
> Dear all,
>
> I am trying to run a protein-ligand simulation as described
Dear all,
I am trying to run a protein-ligand simulation as described in the
tutorial by Justin Lemkul
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/01_pdb2gmx.html
However, while creating a unit cell using editconf command, I encounter a
problem. The output
Hello, Catch ya,
Thank you for your reply. Using "lscpu", the cpu information of the workstation
is shown as:
Architecture: x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):56
On-line CPU(s) list: 0-55
Thread(s) per core:
Den 2019-08-05 kl. 05:48, skrev Anh Vo:
Hi all,
I have searched online and GROMACS documentation for this question but I
haven't found any clear definition yet. Please help me to clarify it.
In the output .edr file, there are PRESS-XX, PRESS-YY and PRESS-ZZ options.
What do they represent? Are
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