Hi All,
I've built Gromacs 2019 on both a CentOS 7 and SLES12 machine.
Built using gcc@7.2.0
Dependencies:
fftw@3.3.8
openmpi@3.1.3
When running "make check" on both machines, I'm getting the same timeout error
for test 29 - see below for extract and attached for full test output
anyone got any i
Hi,
I have two servers with AMD2950X (16 physical cores). One with 16Gb RAM
and RTX2080Ti, the other 32Gb RAM and GTX1080Ti.
I use gromacs 2018.3, compiled on the same way on both of the servers.
I wanted to run two simulations on the same host (8+8cores and GPU0 and
GPU1). They are OK on the
Hello,
So i'm starting to learn about MD simulations and i've done the tutorial of
Lysozyme in Water for Gromacs, my work is to do MD simulations for sugars
using the tool do_glycans and the force field Glycam06, however i don't
know how to generate the .top file?
i would appreciate it if you coul
Thanks a lot, Kevin for your comments and help.
Zeineb
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Hi,
I notice that the flag ''-av'' in gmx analyze does not give the average
value of the set, rather the data file itself.
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On 3/11/19 2:08 PM, Amin Rouy wrote:
Hi,
I notice that the flag ''-av'' in gmx analyze does not give the average
value of the set, rather the data file itself.
As it should. From gmx help analyze:
"Option -av produces the average over the sets."
If you want the average of different sets,
Hi, Mark,
I'd be happy to, as soon as I get a chance.
I know very little about how GROMACS works internally, but I had a few
ideas I wanted to share in the hopes that they might help. One is that
pairwise parameters for electrostatics could be implemented in the same way
that LJ parameters are st
Hi everybody
I want to do one dynamic simulation of one protein
i'm try to minimize the protein in vacum before the simulation runing but
gromacs send me this error:
---
Program: gmx grompp, version 2018.6
Source file: src/gromacs/gmxpreproces
On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote:
Hi everybody
I want to do one dynamic simulation of one protein
i'm try to minimize the protein in vacum before the simulation runing but
gromacs send me this error:
---
Program: gm
If i don't use -maxwarn option they send me the same error.
I see also this:
WARNING 1 [file topol.top, line 23986]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform back
Dear all
How can I make a movie from a protein-ligand simulation in VMD? I opened
complex.pdb and md-fit.trr and the movie is shown but due to the large number
of water molecules it freezes after some frames. How can I remove solvent
molecules from the md-fit.trr? Any other suggestions how to m
On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote:
If i don't use -maxwarn option they send me the same error.
Omitting -maxwarn won't fix problems, but it is a very bad habit to
casually use -maxwarn as it overrides critical problems with your input.
I see also this:
WARNING 1 [fi
On 3/11/19 6:01 PM, mary ko wrote:
Dear all
How can I make a movie from a protein-ligand simulation in VMD? I opened
complex.pdb and md-fit.trr and the movie is shown but due to the large number
of water molecules it freezes after some frames. How can I remove solvent
molecules from the md-
Dear groamcs user,
A system of mine contains two molecule type of A and B in water. Using
gmx trjconv -f out.xtc -o out.last.5ns.trr I first truncated the last 5ns
of the system's XTC file as a TRR file and just selected the non-water
contents so that the TRR file only has A and B. The TRR file is
.trr and .xtc are two different file formats, with the latter being
compressed. Therefore, an .xtc file will be significantly smaller than a
.trr
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, P
Thank you Justin. Is it possible to choose protein and ligand separately (e.g.
1|13) in the trjconv, since I chose protein-ligand subgroup which was taken as
a whole and ligand can not be distinguished individually ? Or should I do any
modifications in VMD ?
On Monday, March 11, 2019, 6:32
Hi dear GROMACS usersI want to calculate hydrophobic interactions and
electrostatic interactions between the protein chains using gromacs trajectory
. Please guide me.Thanks a lot
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