Dear gromacs users,
I wanted to simulate sulphate ions in water using oplsaa force field but I
couldn't find parameters for sulphur and oxygen atoms of sulphate ions in the
oplsaa force field files. Can anyone suggest from where can I get these
parameters?
Charmm force field has the paramete
Hi GROMACS users,
I have some questions: 1- Can I model a carbonnanotube (CNT)
conveying fluid in GROMACS subjected to a magnetic field?2- How can I
check the centerof mass velocity of my system?3- I want to calculate
volumeand water self diffusion coefficient for
Respected sir!
Thanks for your response
I recompile my system(gromacs5.0.7) but the error remain same.
looking for your response to solve this issue.
thank you one again
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Hi ,
Maybe you can try -merge all when using pdb2gmx.
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Hi, gmx users,
I used materials studio to generate a .pdb file containing 160 PTFE chains,
and then modified the oplsaa forcefiled as Justin did. The pdb2gmx
generated right .gro and .top files. But the problem is that it generated
one .itp file for each molecule. Since there are 160 identical m
HIi am making topology of protein ligand complex for calculating binding free
energy. my question is do i need to define state B manually or is there any
automatic method to do that. Second question is i want of number my ligand atom
numbers from the number where protein atom numbers are stopped
Hello,This question is more about the WHAM technique in general, but I take the
liberty to ask it in this forum, hoping somebody can point me in the right
direction.
I am calculating the free energy difference between two wells separated by an
energy barrier using an umbrella potential restraini
Thanks :)
In case anyone else wonders, the highest occupancy atom is taken.
Irem
> On Feb 23, 2016, at 3:04 PM, Mark Abraham wrote:
>
> Hi,
>
> Swap them and see :-)
>
> Mark
>
> On Tue, 23 Feb 2016 20:55 Irem Altan wrote:
>
>> Hi,
>>
>> I have a protein that contains atoms with alternat
Hi,
Swap them and see :-)
Mark
On Tue, 23 Feb 2016 20:55 Irem Altan wrote:
> Hi,
>
> I have a protein that contains atoms with alternate conformations:
>
> ATOM856 SG ACYS A 217 7.649 52.725 28.525 0.58 12.64
>S
> ATOM859 SG BCYS A 217 7.282 54.809 26.839 0.42 1
Hi,
I have a protein that contains atoms with alternate conformations:
ATOM856 SG ACYS A 217 7.649 52.725 28.525 0.58 12.64 S
ATOM859 SG BCYS A 217 7.282 54.809 26.839 0.42 15.97 S
How does pdb2gmx handle this? I checked the .gro file to see that S
Hi,
These questions are quite specific to your problem. There's no way we can
predict what equilibration time will suffice for your system. Your
simulation time also depends on what the aim of your simulations is and
what you hope to observe. That said, current simulations are generally a
couple o
Dear colleagues,
I'm starting to use GROMACS and I'm simulating a system between an RNA binding
protein and a small RNA ligand (a dinucleotide, ~60 atoms) in a cubic box. I
set AMBER99SB-ILDN protein, nucleic AMBER94 as a forcefield, with a tip3p
water model.
This was only to put you in conte
Hi,
As normal, even for coarse-grained simulations, equilibration may require
bigger rearrangements for some starting conditions than others. The usual
advice for http://www.gromacs.org/Documentation/Terminology/Blowing_Up still
applies - particularly to try smaller time steps while relaxing what
Hi all,
I am running an equilibration of a membrane/protein coarse grained
system and got this Segmentation fault error.
---
Reading file equilibration.protein_DPPC.tpr, VERSION 4.6.5 (single
precision)
Using 8 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this
mac
Hi,
Indeed that seems to short. So if one has excluded natural processes, the
artificial ones remain the only possible ones... Your process does have to
include a custom index group, for example... see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
On Tue, Feb
Hi Mark,
Thank you for the suggestions, but I don't think it is because of the PBC
artifacts. I do centered my protein and ligand with "-center -pbc mol"
option. The protein itself looks fine without any breaking. It's just the
ATP that moves out and stays at the outer surface of the protein. I d
On 2/22/16 10:03 PM, Ming Tang wrote:
Thanks Justin,
How about LJ and Coulomb energy?
I want to see the trend of protein energy only. I defined 2 energy group:
protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein
option when using g_energy. Are they VDW and Coulomb fo
On 2/23/16 9:45 AM, Sara Del Galdo wrote:
Hi Gromacs users,
I am using gromacs tool g_sas to calculate protein excluded volumes and I
noticed that it provides significant different excluded volume values when
compared to the new version gmx sasa tool. Does anyone know the reason of
this and wh
Hi Gromacs users,
I am using gromacs tool g_sas to calculate protein excluded volumes and I
noticed that it provides significant different excluded volume values when
compared to the new version gmx sasa tool. Does anyone know the reason of
this and which of the two tool is more reliable?
Thanks i
Hi,
That's still going to need an updated binutils, though.
Mark
On Tue, Feb 23, 2016 at 3:40 PM Szilárd Páll wrote:
> AVX is supported even by gcc 4.4.7 (although admittedly I'm not sure if
> it's functional), so you may want to try -DGMX_SIMD=AVX_256, that will
> waste your hardware a bit le
AVX is supported even by gcc 4.4.7 (although admittedly I'm not sure if
it's functional), so you may want to try -DGMX_SIMD=AVX_256, that will
waste your hardware a bit less.
--
Szilárd
On Tue, Feb 23, 2016 at 3:02 PM, Mark Abraham
wrote:
> Hi,
>
> You can probably use any GROMACS version, if y
Hi,
You can probably use any GROMACS version, if you want it to run slowly and
generate less science for you. Just use cmake -DGMX_SIMD=SSE4.1.
Mark
On Tue, Feb 23, 2016 at 2:47 PM SOUVIK MONDAL wrote:
> Which version of gromacs will be suitable for gcc version 4.4.7?
>
>
>
> - Original Me
Which version of gromacs will be suitable for gcc version 4.4.7?
- Original Message -
From: "Mark Abraham"
To: gmx-us...@gromacs.org
Sent: Tuesday, February 23, 2016 6:05:13 PM
Subject: Re: [gmx-users] Regarding installation problem
Hi,
The simplest thing is to get the latest version
Hi,
The simplest thing is to get the latest version of gcc that your operating
system (e.g. Linux distribution) supports. Sadly, people often sell compute
systems based on "mature, stable, reliable" versions of software, but with
modern hardware, which automatically means that everything is out of
Can u tell what are compilers I need to up-to-date?
- Original Message -
From: "Mark Abraham"
To: gmx-us...@gromacs.org
Sent: Tuesday, February 23, 2016 4:50:52 PM
Subject: Re: [gmx-users] Regarding installation problem
Hi,
On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL
wrote:
> After
Hi,
On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL
wrote:
> After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> the output in that ternimal comes as follows
>
> - The C compiler identification is GNU 4.4.7
> -- The CXX compiler identification is GNU 4.4.7
>
This compiler
After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
the output in that ternimal comes as follows
- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin
Hi,
Yes, I know. That's its job. The only likely relevant part is very near the
end. But first I wanted to see the terminal output - what you saw on the
screen when you ran cmake.
Mark
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The CmakeErroor.log file have following things
Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following
output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_bf3f2/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_bf3f2.dir/b
Hi all,
A post-doctoral position in Computational Physics is currently available
in the Computational mOdelling of NanosCalE and bioPhysical sysTems
(CONCEPT) Lab
(https://beta.iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems)
at IIT - Genoa (ITA) to work on
Hi all,
Is there a friendly Gromacs compatible tool for generating a .gro/.pdb
file using a specific forcefield topology specification within Gromacs
itself? For context:
I¹m in the process of fully parameterising five custom protein residues
for the amber forcefield from ab initio calculations. F
Hi,
Very likely not, but technically the answer can depend how the compiler
toolchain sets up things like dynamic loading of libraries. You can perhaps
explore that effect with the command line tools ldd and objdump on the gmx
executable. You could read the Intel docs, but they'll just say "yes it
Hi,
It sounds like you are observing artefacts from
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan wrote:
> Hi Gromacs Users,
>
> I'm running 20ns MD simulation of a protein kinase with ATP bond. I use
> amber99sb-i
Hi,
On Tue, Feb 23, 2016 at 6:25 AM Raju Lunkad <
r.lun...@students.iiserpune.ac.in> wrote:
> Dear Gromacs users,
> I am trying to run a simulation but I am getting the error regarding the
> domain decomposition.
Which error? People often can't help much without precise information.
Probably yo
Hi,
The limited information you've provided doesn't sound like it is the real
problem. What does the whole cmake terminal output say?
Mark
On Tue, Feb 23, 2016 at 7:38 AM SOUVIK MONDAL wrote:
> Hi
> I have found the following problem regarding gromacs 5.1.2 installation.
> I have installes c
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