Dear Gromacs user's,
Could anybody tell me how to calculate
energy autocorrelation function using Gromacs. I need it to take statistically
uncorrelated snapshots for further calculations or somebody has done the same
using some other method that is available
Hello Justin,
I looked at the energy components. What I find is that Short Range LJ is
highly positive (208522 kJ/mol) . Also the short range coulomb interaction
(-2028.46 kJ/mol) , although negative looks weak (I think so , because an
earlier minimization of a system with methane( oplsaa) in wat
Thanks for the explanation Rossen.I hope mailman gets some more artificial
intelligence in coming future :).cheers,Abhi
> Date: Wed, 14 May 2014 14:33:00 +0200
> From: ros...@kth.se
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Why does the list keep unsubscribing me?
>
> Hi,
>
> Someo
Hi Dear Gromacs Users,
I am running a umbrella samplimg simulation with gromacs 4.6.5, this
simulations is a molecule permeating an ion channel, i decided to use X Y
position restraints 400KJ , but i
am not pretty sure if this kind of bias if a real mistake, i was wondering
if anyone know how to u
On 5/14/14, 8:21 PM, Chetan Mahajan wrote:
Dear All,
While converting LJ parameters from Amber to Gromacs, acpype tool (that is
used for converting Amber input files into those for gromacs) uses
following form:
sigma = 2 * r * 2^(-1/6)
I understand the factor 2^(-1/6), but there is another "
Dear All,
While converting LJ parameters from Amber to Gromacs, acpype tool (that is
used for converting Amber input files into those for gromacs) uses
following form:
sigma = 2 * r * 2^(-1/6)
I understand the factor 2^(-1/6), but there is another "2" that appears in
the beginning. Where is that
Dear All,
While converting LJ parameters from Amber to Gromacs, acpype tool (that is
used for converting Amber input files into those for gromacs) uses
following form:
sigma = 2 * r * 2^(-1/6)
I understand the factor 2^(-1/6), but there is another "2" that appears in
the beginning. Where is that
I just did. It turns out that when there is a charged lipid in the system
(as in my case), charmm-gui increases the effective concentration to
compensate for the system's net charge. I have pasted my discourse with
them below.
My email:
I have a question. I generated a membrane using the charmm-gu
On 5/14/14, 12:06 PM, Ali Khan wrote:
By hand it is about 201 molecules. It is strange that the membrane builder
in charmm-gui gives a different answer for the same box dimensions. I guess
those of us that use the charmm-gui membrane builder should keep this in
mind.
Better yet, please repor
MPI and thread-MPI, as the error messages state are mutually
exclusive, hence passing -ntmpi to the MPI-enabled binary is just
incorrect. I suggest that you read up on the GROMACS parallelization:
www.gromacs.org/Documentation/Acceleration_and_parallelization
Secondly, those MPI messages may mean
By hand it is about 201 molecules. It is strange that the membrane builder
in charmm-gui gives a different answer for the same box dimensions. I guess
those of us that use the charmm-gui membrane builder should keep this in
mind.
On Wed, May 14, 2014 at 11:14 AM, Erik Marklund wrote:
> Hi Ali,
On 5/14/14, 11:11 AM, Andrew Bostick wrote:
Dear Gromacs users
After I calculated the secondary structure of residues from 1 to 59 using
do_dssp during 20 ns MD simulation, I used xpm2ps to show the picture with
ps.m2p.
y-axis is true but x- axis is very long.
My ps.m2p file is as follows:
On 5/14/14, 7:54 AM, elham tazikeh wrote:
dear gromacs users
i did simulate zinc and copper ion on human growth hormone protein
when i saw my md.gro and md.xtc files by VMD software
i found out my system isn,t in the box(cubic)
i tried to solve this problem by :
trjconv -f md.xtc -s md.tpr -o
On 5/14/14, 12:39 AM, sujithkakkat . wrote:
Hello Justin and others,
Thank you for the response . Here are mode details of the system; ( in
the order ; MDP settings, itp and top files) . The system consists of 460
water molecules and 1 CO2 molecule . I am trying to find the free energy
o
Hi Szilárd:
thx for the comments.
The log file in my previous thread comes from command line:
tmp/input> mpirun -np 2 mdrun_mpi -s 4.tpr
[mpiexec@cudaA.compuBio] HYDU_getfullhostname
(./utils/others/others.c:136): getaddrinfo error (hostname: cudaA.compuBio,
error: Name or service not known)
[m
Hi Ali,
And what would you expect in this case, based on the definition of
concentration?
Erik
On 14 May 2014, at 04:11, Ali Khan wrote:
> Sorry Mark,
>
> I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232 potassium
> atoms. Its a small difference, and both methods have the sa
Dear Gromacs users
After I calculated the secondary structure of residues from 1 to 59 using
do_dssp during 20 ns MD simulation, I used xpm2ps to show the picture with
ps.m2p.
y-axis is true but x- axis is very long.
My ps.m2p file is as follows:
; Command line options of xpm2ps override the pa
This just tells that two GPU-s were detected but only the first one
was automatically selected to be used - presumably because you
manually specified the number of ranks (-np or -ntmpi) to be one.
However, your mail contains neither the command line you started mdrun
with, nor (a link to) the log
Hi Mark:
thanks a lot for the messages. In most cases, job failed with following
messages if I used intel MPI to evoke two GPU:
[mpiexec@cudaA.compuBio] HYDU_getfullhostname
(./utils/others/others.c:136): getaddrinfo error (hostname: cudaA.compuBio,
error: Name or service not known)
[mpiexec@cuda
Hi,
Someone else mentioned the same recently.
Automatic removal can happen if someone, e.g. a spammer, sends a mail to
gmx-users-unsubscr...@gromacs.org while faking your email address in the
From: field.
Mailman is now maintained centrally by the university, so I can't dig in
the logs for
dear gromacs users
i did simulate zinc and copper ion on human growth hormone protein
when i saw my md.gro and md.xtc files by VMD software
i found out my system isn,t in the box(cubic)
i tried to solve this problem by :
trjconv -f md.xtc -s md.tpr -o new.xtc -n index.ndx -pbc mol
but there is th
So Google Groups doesn't allow you to import users, right? But I have seen
Gromacs's Google Groups, however it has been abandoned since 2012, I don't
know why. Also, I found another mail list which is better than the three
ones I have mentioned above. It www.gmane.org. It also has statistic of each
Dear Gromacs users,
I am using Test Particle Insertion with Gromacs 4.6.5. The method works
well when I use TIP3P and SPC/E water to obtain the excess chemical
potential of water and I get a reasonable agreement with experimental data.
However, when using TIP5P water the method diverges:
[..
This is the second time in 2 months, that I am unsubscribed from the list and i
have to subscribe again. I just get an email that you have been unsubscribed
from the list?
How can I get unsubscribed without my intervention is beyond understanding?
--
OK, but with Berendsen you're also not observing physics. Your call.
Mark
On Wed, May 14, 2014 at 3:50 AM, Steven Neumann wrote:
> Thanks a lot! Berendsen barostat works well with V-rescale using REMD, no
> crashes observed.
>
>
> On Tue, May 13, 2014 at 2:08 PM, Mark Abraham >wrote:
>
> > On
Hi,
Nobody can tell unless you upload .log files and mdrun command lines
somewhere
Mark
On Wed, May 14, 2014 at 7:03 AM, Albert wrote:
> Hello:
>
> I've compiled Gromacs in a GPU machine with two GTX780Ti with following
> command:
>
> env CC=icc F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/soft/inte
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